Re: [ccp4bb] crystallization optimization

[Frank von Delft]

Actually, you should try /increasing/ the protein concentration - a 
lot.  But be prepared to drop the precipitant concentration to almost 
nothing (1 or 2% isn't "low").


To understand why, look at the phase diagram and what we assume about 
vapour diffusion.  (Which I'm assuming is what you're doing.)



On 12/07/2017 06:28, Vicky Tsirkone wrote:

Dear Patrick,

You may reduce the protein concentation, as well.
Another option could be the *streak seeding* by exploiting the drop of 
your initial condition.


Good luck,

V.T.

On Mon, Jul 10, 2017 at 7:17 PM, Patrick Shaw Stewart 
> wrote:



Microseed them into two or three random screens.

Search for MMS and rMMS online.

Good luck

Patrick




On 10 July 2017 at 15:47, Liuqing Chen <519198...@163.com
> wrote:

hello everyone!
I get a condition (10% w/v PEG 6000, 100mm HEPES PH7.0) in
which my protein grow small  needle like crystals, how can i
optimize it to get bigger crystals?  the attach is the
crystals  figure.
thanks in advance
sincerely
Liuqing Chen




-- 
patr...@douglas.co.uk  Douglas

Instruments Ltd.
 Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
 Directors: Peter Baldock, Patrick Shaw Stewart

http://www.douglas.co.uk
 Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034

 Regd. England 2177994, VAT Reg. GB 480 7371 36

Re: [ccp4bb] crystallization optimization

[Vicky Tsirkone]

Dear Patrick,

You may reduce the protein concentation, as well.
Another option could be the *streak seeding* by exploiting the drop of your
initial condition.

Good luck,

V.T.

On Mon, Jul 10, 2017 at 7:17 PM, Patrick Shaw Stewart  wrote:

>
> Microseed them into two or three random screens.
>
> Search for MMS and rMMS online.
>
> Good luck
>
> Patrick
>
>
>
>
> On 10 July 2017 at 15:47, Liuqing Chen <519198...@163.com> wrote:
>
>> hello everyone!
>> I get a condition (10% w/v PEG 6000, 100mm HEPES PH7.0) in which my
>> protein grow small  needle like crystals, how can i optimize it to get
>> bigger crystals?  the attach is the crystals  figure.
>> thanks in advance
>> sincerely
>> Liuqing Chen
>>
>
>
>
> --
>  patr...@douglas.co.ukDouglas Instruments Ltd.
>  Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
>  Directors: Peter Baldock, Patrick Shaw Stewart
>
>  http://www.douglas.co.uk
>  Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
> <(877)%20225-2034>
>  Regd. England 2177994, VAT Reg. GB 480 7371 36
>

Re: [ccp4bb] Problem with a cell content

[Eleanor Dodson]

Absolutely agree
Eleanor

On 11 July 2017 at 22:06, Keller, Jacob  wrote:

> Still seems to me that the resolution could and should be pushed a little
> further at least—CC1/2 is still high, completeness is good, I/sigma also is
> good. Why not extend a little further, say to where one of these values
> gets too low? Might improve the maps a bit.
>
>
>
> JPK
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of 
> *Koromyslova,
> Anna
> *Sent:* Tuesday, July 11, 2017 3:37 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
>
> *Subject:* Re: [ccp4bb] Problem with a cell content
>
>
>
> Sorry for the confusion, NCS was found only in a dataset where the cell
> dimensions were twice bigger regardless of the sp, and with a dimer as a
> solution. The solvent content was the same.
>
> Peak Distance   Vector
>
> 73.3% 143.8Å:   FRAC +0.000 +0.000 -0.500   (ORTH   -0.00.0 -143.8).
>
> There was no NCS in a dataset with a smaller unit cell and sp P6222.
>
> Thank you!
>
>
>
> Best regards,
>
>
>
> Anna
>
>
>
>
>
>
>
> Dr. Anna Koromyslova, Postdoctoral researcher
>
> German Cancer Research Center (DKFZ), F150
>
> Im Neuenheimer Feld 242
>
> D-69120 Heidelberg
>
> Germany
>
>
>
>
>
> *From: *Eleanor Dodson 
> *Date: *Tuesday, July 11, 2017 at 8:17 PM
> *To: *"Koromyslova, Anna" 
> *Cc: *"CCP4BB@JISCMAIL.AC.UK" 
> *Subject: *Re: [ccp4bb] Problem with a cell content
>
>
>
> So SG  could be P31 2 2
>
> What is the height of NCS vector v origin?
>
> Eleanor
>
> Look at hklview to see hk i  sections. Obviously all l = odd will be weak.
>
>
>
>
>
> On 11 July 2017 at 19:12, Koromyslova, Anna  heidelberg.de> wrote:
>
> Dear Eleanor,
>
>
>
> NCS translation vector = 0 0 -0.5 in the final sp P6222, and in P622 or
> C121. All had the same solution.
>
> The protein tends to form a homodimer and if I use P1 space group
> molecular replacement can find several dimers, there is no translational
> ncs found during MR, but still solvent cell content was similarly high.
>
> Within a protein monomer there are no similar domains.
>
>
>
> Best regards,
>
> Anna
>
>
>
>
>
>
>
> *From: *CCP4 bulletin board  on behalf of Eleanor
> Dodson 
> *Reply-To: *Eleanor Dodson 
> *Date: *Tuesday, July 11, 2017 at 7:29 PM
> *To: *"CCP4BB@JISCMAIL.AC.UK" 
> *Subject: *Re: [ccp4bb] Problem with a cell content
>
>
>
> This is very strange . If you have a large non- crystallographic
> translation vector you would expect either to have two molecules in the
> asymmetric unit or your one molecule must have two very similar domains?
>
> What is the n-c translation vector?
>
>
>
> Could you have assigned too high symmetry ? SG maybe P 62? That could
> explain the packing clashes Z scores of 27 are pretty good.
>
>
>
> Eleanor
>
>
>
>
>
> On 11 July 2017 at 18:05, Oganesyan, Vaheh 
> wrote:
>
> Похоже, что вы уже решили структуру. Почему вас беспокоит плотность ваших
> кристаллов? Кристаллы бывают разные.
>
>
>
> First of all Fab by itself is already almost 50 kDa, so complex with
> antigen should be more than 50 kDa. Because you already solved the
> structure calculate the molecular mass based on your pdb file and rerun
> Matthews with correct mass. New numbers may be quite a bit different. Good
> indication of relatively low crystal density and consequently loose packing
> is the resolution of your data set. If you did not throw away data beyond
> 2.9A I’d suggest use them all. The reflections are too valuable to throw
> away. If data beyond some resolution is weak then they will have low
> contribution to the structure. Best if you calculate electron density maps
> at different resolutions at the end of refinement, compare them and use
> resolution that makes difference.
>
>
>
>
>
>
>
> *Regards,*
>
>
>
> *Vaheh*
>
> *8-5851*
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of 
> *Koromyslova,
> Anna
> *Sent:* Tuesday, July 11, 2017 12:32 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Problem with a cell content
>
>
>
> Dear CCP4 members,
>
>
>
> I am working on a structure of a protein in complex with an antibody
> fragment (approx. 50kDa together). Molecular replacement with closely
> related proteins always comes up with one complex in the asymmetric unit,
> although MW of protein to which Matthews applies is 125kDa and corresponds
> to two complexes.
>
> Phaser gives two warnings:
>
> Large non-origin Patterson peak indicates that translational NCS is
> present.
>
> Solutions with Z-scores greater than 27.2 (the threshold indicating a
> definite solution) were rejected for failing packing test
>
>
>
> I couldn’t get a solution with two subunits although I have tried multiple
> combinations including only conserved parts of both proteins and different

Re: [ccp4bb] Problem with a cell content

[Keller, Jacob]

Still seems to me that the resolution could and should be pushed a little 
further at least—CC1/2 is still high, completeness is good, I/sigma also is 
good. Why not extend a little further, say to where one of these values gets 
too low? Might improve the maps a bit.

JPK

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
Koromyslova, Anna
Sent: Tuesday, July 11, 2017 3:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Problem with a cell content

Sorry for the confusion, NCS was found only in a dataset where the cell 
dimensions were twice bigger regardless of the sp, and with a dimer as a 
solution. The solvent content was the same.
Peak Distance   Vector
73.3% 143.8Å:   FRAC +0.000 +0.000 -0.500   (ORTH   -0.00.0 -143.8).
There was no NCS in a dataset with a smaller unit cell and sp P6222.
Thank you!

Best regards,

Anna



Dr. Anna Koromyslova, Postdoctoral researcher
German Cancer Research Center (DKFZ), F150
Im Neuenheimer Feld 242
D-69120 Heidelberg
Germany


From: Eleanor Dodson 
>
Date: Tuesday, July 11, 2017 at 8:17 PM
To: "Koromyslova, Anna" 
>
Cc: "CCP4BB@JISCMAIL.AC.UK" 
>
Subject: Re: [ccp4bb] Problem with a cell content

So SG  could be P31 2 2
What is the height of NCS vector v origin?
Eleanor
Look at hklview to see hk i  sections. Obviously all l = odd will be weak.


On 11 July 2017 at 19:12, Koromyslova, Anna 
> 
wrote:
Dear Eleanor,

NCS translation vector = 0 0 -0.5 in the final sp P6222, and in P622 or C121. 
All had the same solution.
The protein tends to form a homodimer and if I use P1 space group molecular 
replacement can find several dimers, there is no translational ncs found during 
MR, but still solvent cell content was similarly high.
Within a protein monomer there are no similar domains.

Best regards,
Anna



From: CCP4 bulletin board > 
on behalf of Eleanor Dodson 
>
Reply-To: Eleanor Dodson 
>
Date: Tuesday, July 11, 2017 at 7:29 PM
To: "CCP4BB@JISCMAIL.AC.UK" 
>
Subject: Re: [ccp4bb] Problem with a cell content

This is very strange . If you have a large non- crystallographic translation 
vector you would expect either to have two molecules in the asymmetric unit or 
your one molecule must have two very similar domains?
What is the n-c translation vector?

Could you have assigned too high symmetry ? SG maybe P 62? That could explain 
the packing clashes Z scores of 27 are pretty good.

Eleanor


On 11 July 2017 at 18:05, Oganesyan, Vaheh 
> wrote:
Похоже, что вы уже решили структуру. Почему вас беспокоит плотность ваших 
кристаллов? Кристаллы бывают разные.

First of all Fab by itself is already almost 50 kDa, so complex with antigen 
should be more than 50 kDa. Because you already solved the structure calculate 
the molecular mass based on your pdb file and rerun Matthews with correct mass. 
New numbers may be quite a bit different. Good indication of relatively low 
crystal density and consequently loose packing is the resolution of your data 
set. If you did not throw away data beyond 2.9A I’d suggest use them all. The 
reflections are too valuable to throw away. If data beyond some resolution is 
weak then they will have low contribution to the structure. Best if you 
calculate electron density maps at different resolutions at the end of 
refinement, compare them and use resolution that makes difference.



Regards,

Vaheh
8-5851

From: CCP4 bulletin board 
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
Koromyslova, Anna
Sent: Tuesday, July 11, 2017 12:32 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Problem with a cell content

Dear CCP4 members,

I am working on a structure of a protein in complex with an antibody fragment 
(approx. 50kDa together). Molecular replacement with closely related proteins 
always comes up with one complex in the asymmetric unit, although MW of protein 
to which Matthews applies is 125kDa and corresponds to two complexes.
Phaser gives two warnings:
Large non-origin Patterson peak indicates that translational NCS is present.
Solutions with Z-scores greater than 27.2 (the threshold indicating a definite 
solution) were rejected for failing packing test

I couldn’t get a solution with two subunits although I have tried multiple 
combinations including only conserved parts of both proteins and different 
space groups including P1. Phenix Autobuild also yielded 

Re: [ccp4bb] Problem with a cell content

[Eleanor Dodson]

That makes sense then - you have solved it am sure.
Eleanor

On 11 July 2017 at 20:36, Koromyslova, Anna <
a.koromysl...@dkfz-heidelberg.de> wrote:

> Sorry for the confusion, NCS was found only in a dataset where the cell
> dimensions were twice bigger regardless of the sp, and with a dimer as a
> solution. The solvent content was the same.
>
> Peak Distance   Vector
>
> 73.3% 143.8Å:   FRAC +0.000 +0.000 -0.500   (ORTH   -0.00.0 -143.8).
>
> There was no NCS in a dataset with a smaller unit cell and sp P6222.
>
> Thank you!
>
>
>
> Best regards,
>
>
>
> Anna
>
>
>
>
>
>
>
> Dr. Anna Koromyslova, Postdoctoral researcher
>
> German Cancer Research Center (DKFZ), F150
>
> Im Neuenheimer Feld 242
>
> D-69120 Heidelberg
>
> Germany
>
>
>
>
>
> *From: *Eleanor Dodson 
> *Date: *Tuesday, July 11, 2017 at 8:17 PM
> *To: *"Koromyslova, Anna" 
> *Cc: *"CCP4BB@JISCMAIL.AC.UK" 
>
> *Subject: *Re: [ccp4bb] Problem with a cell content
>
>
>
> So SG  could be P31 2 2
>
> What is the height of NCS vector v origin?
>
> Eleanor
>
> Look at hklview to see hk i  sections. Obviously all l = odd will be weak.
>
>
>
>
>
> On 11 July 2017 at 19:12, Koromyslova, Anna  heidelberg.de> wrote:
>
> Dear Eleanor,
>
>
>
> NCS translation vector = 0 0 -0.5 in the final sp P6222, and in P622 or
> C121. All had the same solution.
>
> The protein tends to form a homodimer and if I use P1 space group
> molecular replacement can find several dimers, there is no translational
> ncs found during MR, but still solvent cell content was similarly high.
>
> Within a protein monomer there are no similar domains.
>
>
>
> Best regards,
>
> Anna
>
>
>
>
>
>
>
> *From: *CCP4 bulletin board  on behalf of Eleanor
> Dodson 
> *Reply-To: *Eleanor Dodson 
> *Date: *Tuesday, July 11, 2017 at 7:29 PM
> *To: *"CCP4BB@JISCMAIL.AC.UK" 
> *Subject: *Re: [ccp4bb] Problem with a cell content
>
>
>
> This is very strange . If you have a large non- crystallographic
> translation vector you would expect either to have two molecules in the
> asymmetric unit or your one molecule must have two very similar domains?
>
> What is the n-c translation vector?
>
>
>
> Could you have assigned too high symmetry ? SG maybe P 62? That could
> explain the packing clashes Z scores of 27 are pretty good.
>
>
>
> Eleanor
>
>
>
>
>
> On 11 July 2017 at 18:05, Oganesyan, Vaheh 
> wrote:
>
> Похоже, что вы уже решили структуру. Почему вас беспокоит плотность ваших
> кристаллов? Кристаллы бывают разные.
>
>
>
> First of all Fab by itself is already almost 50 kDa, so complex with
> antigen should be more than 50 kDa. Because you already solved the
> structure calculate the molecular mass based on your pdb file and rerun
> Matthews with correct mass. New numbers may be quite a bit different. Good
> indication of relatively low crystal density and consequently loose packing
> is the resolution of your data set. If you did not throw away data beyond
> 2.9A I’d suggest use them all. The reflections are too valuable to throw
> away. If data beyond some resolution is weak then they will have low
> contribution to the structure. Best if you calculate electron density maps
> at different resolutions at the end of refinement, compare them and use
> resolution that makes difference.
>
>
>
>
>
>
>
> *Regards,*
>
>
>
> *Vaheh*
>
> *8-5851*
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of 
> *Koromyslova,
> Anna
> *Sent:* Tuesday, July 11, 2017 12:32 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Problem with a cell content
>
>
>
> Dear CCP4 members,
>
>
>
> I am working on a structure of a protein in complex with an antibody
> fragment (approx. 50kDa together). Molecular replacement with closely
> related proteins always comes up with one complex in the asymmetric unit,
> although MW of protein to which Matthews applies is 125kDa and corresponds
> to two complexes.
>
> Phaser gives two warnings:
>
> Large non-origin Patterson peak indicates that translational NCS is
> present.
>
> Solutions with Z-scores greater than 27.2 (the threshold indicating a
> definite solution) were rejected for failing packing test
>
>
>
> I couldn’t get a solution with two subunits although I have tried multiple
> combinations including only conserved parts of both proteins and different
> space groups including P1. Phenix Autobuild also yielded only one complex.
>
>
>
> So, the question is whether I can use that structure as is despite very
> high solvent content (80%) or should I try smth else. I would be very
> grateful for any suggestions.
>
>
>
> When the solution with a single complex is refined the statistics are the
> following:
>
>
>
> R-work  0.2129
>
> R-free  0.2459
>
> Matthews Coefficient: 6.22
>
> 

Re: [ccp4bb] Problem with a cell content

[Koromyslova, Anna]

Sorry for the confusion, NCS was found only in a dataset where the cell 
dimensions were twice bigger regardless of the sp, and with a dimer as a 
solution. The solvent content was the same.
Peak Distance   Vector
73.3% 143.8Å:   FRAC +0.000 +0.000 -0.500   (ORTH   -0.00.0 -143.8).
There was no NCS in a dataset with a smaller unit cell and sp P6222.
Thank you!

Best regards,

Anna



Dr. Anna Koromyslova, Postdoctoral researcher
German Cancer Research Center (DKFZ), F150
Im Neuenheimer Feld 242
D-69120 Heidelberg
Germany


From: Eleanor Dodson 
Date: Tuesday, July 11, 2017 at 8:17 PM
To: "Koromyslova, Anna" 
Cc: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: [ccp4bb] Problem with a cell content

So SG  could be P31 2 2
What is the height of NCS vector v origin?
Eleanor
Look at hklview to see hk i  sections. Obviously all l = odd will be weak.



On 11 July 2017 at 19:12, Koromyslova, Anna 
> 
wrote:
Dear Eleanor,

NCS translation vector = 0 0 -0.5 in the final sp P6222, and in P622 or C121. 
All had the same solution.
The protein tends to form a homodimer and if I use P1 space group molecular 
replacement can find several dimers, there is no translational ncs found during 
MR, but still solvent cell content was similarly high.
Within a protein monomer there are no similar domains.

Best regards,
Anna



From: CCP4 bulletin board > 
on behalf of Eleanor Dodson 
>
Reply-To: Eleanor Dodson 
>
Date: Tuesday, July 11, 2017 at 7:29 PM
To: "CCP4BB@JISCMAIL.AC.UK" 
>
Subject: Re: [ccp4bb] Problem with a cell content

This is very strange . If you have a large non- crystallographic translation 
vector you would expect either to have two molecules in the asymmetric unit or 
your one molecule must have two very similar domains?
What is the n-c translation vector?

Could you have assigned too high symmetry ? SG maybe P 62? That could explain 
the packing clashes Z scores of 27 are pretty good.

Eleanor


On 11 July 2017 at 18:05, Oganesyan, Vaheh 
> wrote:
Похоже, что вы уже решили структуру. Почему вас беспокоит плотность ваших 
кристаллов? Кристаллы бывают разные.

First of all Fab by itself is already almost 50 kDa, so complex with antigen 
should be more than 50 kDa. Because you already solved the structure calculate 
the molecular mass based on your pdb file and rerun Matthews with correct mass. 
New numbers may be quite a bit different. Good indication of relatively low 
crystal density and consequently loose packing is the resolution of your data 
set. If you did not throw away data beyond 2.9A I’d suggest use them all. The 
reflections are too valuable to throw away. If data beyond some resolution is 
weak then they will have low contribution to the structure. Best if you 
calculate electron density maps at different resolutions at the end of 
refinement, compare them and use resolution that makes difference.



Regards,

Vaheh
8-5851

From: CCP4 bulletin board 
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
Koromyslova, Anna
Sent: Tuesday, July 11, 2017 12:32 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Problem with a cell content

Dear CCP4 members,

I am working on a structure of a protein in complex with an antibody fragment 
(approx. 50kDa together). Molecular replacement with closely related proteins 
always comes up with one complex in the asymmetric unit, although MW of protein 
to which Matthews applies is 125kDa and corresponds to two complexes.
Phaser gives two warnings:
Large non-origin Patterson peak indicates that translational NCS is present.
Solutions with Z-scores greater than 27.2 (the threshold indicating a definite 
solution) were rejected for failing packing test

I couldn’t get a solution with two subunits although I have tried multiple 
combinations including only conserved parts of both proteins and different 
space groups including P1. Phenix Autobuild also yielded only one complex.

So, the question is whether I can use that structure as is despite very high 
solvent content (80%) or should I try smth else. I would be very grateful for 
any suggestions.

When the solution with a single complex is refined the statistics are the 
following:

R-work  0.2129
R-free  0.2459
Matthews Coefficient: 6.22
Percentage Solvent: 80.22
Resolution range (Å)  48.34  - 2.9 (2.98  - 2.9)
Space group P 62 2 2
Unit cell  167.45 167.45 143.538 90 90 120
Multiplicity  19.1 (18.3)
Completeness (%)

Re: [ccp4bb] Granada Crystallization Boxes?

[Gloria Borgstahl]

Triana is no longer making or selling them

On Tue, Jul 11, 2017 at 1:39 PM, Diana Tomchick <
diana.tomch...@utsouthwestern.edu> wrote:

> You can continue to buy new ones from Tirana Science & Technology, which
> is a Spanish company.
>
> http://www.trianatech.com/index.php?option=com_content;
> view=article=65=88=en
>
> Diana
>
> **
> Diana R. Tomchick
> Professor
> Departments of Biophysics and Biochemistry
> University of Texas Southwestern Medical Center
> 5323 Harry Hines Blvd.
> Rm. ND10.214A
> Dallas, TX 75390-8816
> diana.tomch...@utsouthwestern.edu
> (214) 645-6383 (phone)
> (214) 645-6353 (fax)
>
> On Jul 11, 2017, at 1:04 PM, Gloria Borgstahl 
> wrote:
>
> I have recently found out that these are no longer being manufactured or
> sold commercially.  But, as fortune has it, we have just been funded to fly
> some large quartz capillaries crystallization experimente up to the
> International Space Station for neutron crystallography.  Our experimental
> design is to fly the experiments in the Granada Crystallation Boxes!  NASA
> has already approved the 3x10x0.5 cm plastic Granada boxes for flights.
> Does anyone have any in their lab supplies that they do not plan to use?
> We would be willing to buy them from you!  Thanks, Gloria
>
>
> --
>
> UT Southwestern
>
> Medical Center
>
> The future of medicine, today.
>

Re: [ccp4bb] Granada Crystallization Boxes?

[Diana Tomchick]

Sorry, that’s Triana Science & Technology (darn automatic spell-check!).

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
University of Texas Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

On Jul 11, 2017, at 1:39 PM, Diana Tomchick 
> 
wrote:

You can continue to buy new ones from Tirana Science & Technology, which is a 
Spanish company.

http://www.trianatech.com/index.php?option=com_content=article=65=88=en

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
University of Texas Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

On Jul 11, 2017, at 1:04 PM, Gloria Borgstahl 
> wrote:

I have recently found out that these are no longer being manufactured or sold 
commercially.  But, as fortune has it, we have just been funded to fly some 
large quartz capillaries crystallization experimente up to the International 
Space Station for neutron crystallography.  Our experimental design is to fly 
the experiments in the Granada Crystallation Boxes!  NASA has already approved 
the 3x10x0.5 cm plastic Granada boxes for flights.   Does anyone have any in 
their lab supplies that they do not plan to use?  We would be willing to buy 
them from you!  Thanks, Gloria




UT Southwestern


Medical Center



The future of medicine, today.

Re: [ccp4bb] Granada Crystallization Boxes?

[Diana Tomchick]

You can continue to buy new ones from Tirana Science & Technology, which is a 
Spanish company.

http://www.trianatech.com/index.php?option=com_content=article=65=88=en

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
University of Texas Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

On Jul 11, 2017, at 1:04 PM, Gloria Borgstahl 
> wrote:

I have recently found out that these are no longer being manufactured or sold 
commercially.  But, as fortune has it, we have just been funded to fly some 
large quartz capillaries crystallization experimente up to the International 
Space Station for neutron crystallography.  Our experimental design is to fly 
the experiments in the Granada Crystallation Boxes!  NASA has already approved 
the 3x10x0.5 cm plastic Granada boxes for flights.   Does anyone have any in 
their lab supplies that they do not plan to use?  We would be willing to buy 
them from you!  Thanks, Gloria




UT Southwestern


Medical Center



The future of medicine, today.

Re: [ccp4bb] Problem with a cell content

[Eleanor Dodson]

So SG  could be P31 2 2

What is the height of NCS vector v origin?
Eleanor

Look at hklview to see hk i  sections. Obviously all l = odd will be weak.




On 11 July 2017 at 19:12, Koromyslova, Anna <
a.koromysl...@dkfz-heidelberg.de> wrote:

> Dear Eleanor,
>
>
>
> NCS translation vector = 0 0 -0.5 in the final sp P6222, and in P622 or
> C121. All had the same solution.
>
> The protein tends to form a homodimer and if I use P1 space group
> molecular replacement can find several dimers, there is no translational
> ncs found during MR, but still solvent cell content was similarly high.
>
> Within a protein monomer there are no similar domains.
>
>
>
> Best regards,
>
> Anna
>
>
>
>
>
>
>
> *From: *CCP4 bulletin board  on behalf of Eleanor
> Dodson 
> *Reply-To: *Eleanor Dodson 
> *Date: *Tuesday, July 11, 2017 at 7:29 PM
> *To: *"CCP4BB@JISCMAIL.AC.UK" 
> *Subject: *Re: [ccp4bb] Problem with a cell content
>
>
>
> This is very strange . If you have a large non- crystallographic
> translation vector you would expect either to have two molecules in the
> asymmetric unit or your one molecule must have two very similar domains?
>
> What is the n-c translation vector?
>
>
>
> Could you have assigned too high symmetry ? SG maybe P 62? That could
> explain the packing clashes Z scores of 27 are pretty good.
>
>
>
> Eleanor
>
>
>
>
>
> On 11 July 2017 at 18:05, Oganesyan, Vaheh 
> wrote:
>
> Похоже, что вы уже решили структуру. Почему вас беспокоит плотность ваших
> кристаллов? Кристаллы бывают разные.
>
>
>
> First of all Fab by itself is already almost 50 kDa, so complex with
> antigen should be more than 50 kDa. Because you already solved the
> structure calculate the molecular mass based on your pdb file and rerun
> Matthews with correct mass. New numbers may be quite a bit different. Good
> indication of relatively low crystal density and consequently loose packing
> is the resolution of your data set. If you did not throw away data beyond
> 2.9A I’d suggest use them all. The reflections are too valuable to throw
> away. If data beyond some resolution is weak then they will have low
> contribution to the structure. Best if you calculate electron density maps
> at different resolutions at the end of refinement, compare them and use
> resolution that makes difference.
>
>
>
>
>
>
>
> *Regards,*
>
>
>
> *Vaheh*
>
> *8-5851*
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of 
> *Koromyslova,
> Anna
> *Sent:* Tuesday, July 11, 2017 12:32 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Problem with a cell content
>
>
>
> Dear CCP4 members,
>
>
>
> I am working on a structure of a protein in complex with an antibody
> fragment (approx. 50kDa together). Molecular replacement with closely
> related proteins always comes up with one complex in the asymmetric unit,
> although MW of protein to which Matthews applies is 125kDa and corresponds
> to two complexes.
>
> Phaser gives two warnings:
>
> Large non-origin Patterson peak indicates that translational NCS is
> present.
>
> Solutions with Z-scores greater than 27.2 (the threshold indicating a
> definite solution) were rejected for failing packing test
>
>
>
> I couldn’t get a solution with two subunits although I have tried multiple
> combinations including only conserved parts of both proteins and different
> space groups including P1. Phenix Autobuild also yielded only one complex.
>
>
>
> So, the question is whether I can use that structure as is despite very
> high solvent content (80%) or should I try smth else. I would be very
> grateful for any suggestions.
>
>
>
> When the solution with a single complex is refined the statistics are the
> following:
>
>
>
> R-work  0.2129
>
> R-free  0.2459
>
> Matthews Coefficient: 6.22
>
> Percentage Solvent: 80.22
>
> Resolution range (Å)  48.34  - 2.9 (2.98  - 2.9)
>
> Space group P 62 2 2
>
> Unit cell  167.45 167.45 143.538 90 90 120
>
> Multiplicity  19.1 (18.3)
>
> Completeness (%)99.44 (94.39)
>
> Mean I/sigma(I) 24.59 (2.71)
>
> Wilson B-factor64.28
>
> R-merge   0.1256 (1.186)
>
> R-meas   0.1291
>
> CC1/2 0.999 (0.85)
>
> CC*1 (0.959)
>
>
>
> Thank you very much for your help,
>
>
>
> Anna
>
>
>
>
>
> Dr. Anna Koromyslova, Postdoctoral researcher
>
> German Cancer Research Center (DKFZ), F150
>
> Im Neuenheimer Feld 242
>
> D-69120 Heidelberg
>
> Germany
>
>
>
> To the extent this electronic communication or any of its attachments
> contain information that is not in the public domain, such information is
> considered by MedImmune to be confidential and proprietary. This
> communication is expected to be read and/or used only by 

Re: [ccp4bb] Problem with a cell content

[Koromyslova, Anna]

Dear Eleanor,

NCS translation vector = 0 0 -0.5 in the final sp P6222, and in P622 or C121. 
All had the same solution.
The protein tends to form a homodimer and if I use P1 space group molecular 
replacement can find several dimers, there is no translational ncs found during 
MR, but still solvent cell content was similarly high.
Within a protein monomer there are no similar domains.

Best regards,
Anna



From: CCP4 bulletin board  on behalf of Eleanor Dodson 

Reply-To: Eleanor Dodson 
Date: Tuesday, July 11, 2017 at 7:29 PM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: [ccp4bb] Problem with a cell content

This is very strange . If you have a large non- crystallographic translation 
vector you would expect either to have two molecules in the asymmetric unit or 
your one molecule must have two very similar domains?
What is the n-c translation vector?

Could you have assigned too high symmetry ? SG maybe P 62? That could explain 
the packing clashes Z scores of 27 are pretty good.

Eleanor


On 11 July 2017 at 18:05, Oganesyan, Vaheh 
> wrote:
Похоже, что вы уже решили структуру. Почему вас беспокоит плотность ваших 
кристаллов? Кристаллы бывают разные.

First of all Fab by itself is already almost 50 kDa, so complex with antigen 
should be more than 50 kDa. Because you already solved the structure calculate 
the molecular mass based on your pdb file and rerun Matthews with correct mass. 
New numbers may be quite a bit different. Good indication of relatively low 
crystal density and consequently loose packing is the resolution of your data 
set. If you did not throw away data beyond 2.9A I’d suggest use them all. The 
reflections are too valuable to throw away. If data beyond some resolution is 
weak then they will have low contribution to the structure. Best if you 
calculate electron density maps at different resolutions at the end of 
refinement, compare them and use resolution that makes difference.



Regards,

Vaheh
8-5851

From: CCP4 bulletin board 
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
Koromyslova, Anna
Sent: Tuesday, July 11, 2017 12:32 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Problem with a cell content

Dear CCP4 members,

I am working on a structure of a protein in complex with an antibody fragment 
(approx. 50kDa together). Molecular replacement with closely related proteins 
always comes up with one complex in the asymmetric unit, although MW of protein 
to which Matthews applies is 125kDa and corresponds to two complexes.
Phaser gives two warnings:
Large non-origin Patterson peak indicates that translational NCS is present.
Solutions with Z-scores greater than 27.2 (the threshold indicating a definite 
solution) were rejected for failing packing test

I couldn’t get a solution with two subunits although I have tried multiple 
combinations including only conserved parts of both proteins and different 
space groups including P1. Phenix Autobuild also yielded only one complex.

So, the question is whether I can use that structure as is despite very high 
solvent content (80%) or should I try smth else. I would be very grateful for 
any suggestions.

When the solution with a single complex is refined the statistics are the 
following:

R-work  0.2129
R-free  0.2459
Matthews Coefficient: 6.22
Percentage Solvent: 80.22
Resolution range (Å)  48.34  - 2.9 (2.98  - 2.9)
Space group P 62 2 2
Unit cell  167.45 167.45 143.538 90 90 120
Multiplicity  19.1 (18.3)
Completeness (%)99.44 (94.39)
Mean I/sigma(I) 24.59 (2.71)
Wilson B-factor64.28
R-merge   0.1256 (1.186)
R-meas   0.1291
CC1/2 0.999 (0.85)
CC*1 (0.959)

Thank you very much for your help,

Anna


Dr. Anna Koromyslova, Postdoctoral researcher
German Cancer Research Center (DKFZ), F150
Im Neuenheimer Feld 242
D-69120 Heidelberg
Germany

To the extent this electronic communication or any of its attachments contain 
information that is not in the public domain, such information is considered by 
MedImmune to be confidential and proprietary. This communication is expected to 
be read and/or used only by the individual(s) for whom it is intended. If you 
have received this electronic communication in error, please reply to the 
sender advising of the error in transmission and delete the original message 
and any accompanying documents from your system immediately, without copying, 
reviewing or otherwise using them for any purpose. Thank you for your 
cooperation.

[ccp4bb] Granada Crystallization Boxes?

[Gloria Borgstahl]

I have recently found out that these are no longer being manufactured or
sold commercially.  But, as fortune has it, we have just been funded to fly
some large quartz capillaries crystallization experimente up to the
International Space Station for neutron crystallography.  Our experimental
design is to fly the experiments in the Granada Crystallation Boxes!  NASA
has already approved the 3x10x0.5 cm plastic Granada boxes for flights.
Does anyone have any in their lab supplies that they do not plan to use?
We would be willing to buy them from you!  Thanks, Gloria

Re: [ccp4bb] Problem with a cell content

[Oganesyan, Vaheh]

Anna,

Eleanor is raising very important question: if you have NCS then there should 
be another similar entity in the asu. Have you detected off origin peak while 
using your final P6222 or lower sg?


From: Koromyslova, Anna [mailto:a.koromysl...@dkfz-heidelberg.de]
Sent: Tuesday, July 11, 2017 1:38 PM
To: Oganesyan, Vaheh; Phil Jeffrey; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Problem with a cell content

Dear Vaheh and Phil,

Sorry, I was a bit misleading – antibody fragment I used is a nanobody (VHH, 
15kDa). I was worried about the cell content because when I started the pdb 
deposition, there was a warning that solvent content is expected to be below 
80%, so I thought maybe I missed a correct solution. But if that’s acceptable 
value the problem is solved.
Thank you for the quick answer and the suggestion about the resolution!

Best regards,

Anna

Dr. Anna Koromyslova, Postdoctoral researcher
German Cancer Research Center (DKFZ), F150
Im Neuenheimer Feld 242
D-69120 Heidelberg
Germany


From: CCP4 bulletin board > 
on behalf of "Oganesyan, Vaheh" 
>
Reply-To: "Oganesyan, Vaheh" 
>
Date: Tuesday, July 11, 2017 at 7:05 PM
To: "CCP4BB@JISCMAIL.AC.UK" 
>
Subject: Re: [ccp4bb] Problem with a cell content

Похоже, что вы уже решили структуру. Почему вас беспокоит плотность ваших 
кристаллов? Кристаллы бывают разные.

First of all Fab by itself is already almost 50 kDa, so complex with antigen 
should be more than 50 kDa. Because you already solved the structure calculate 
the molecular mass based on your pdb file and rerun Matthews with correct mass. 
New numbers may be quite a bit different. Good indication of relatively low 
crystal density and consequently loose packing is the resolution of your data 
set. If you did not throw away data beyond 2.9A I’d suggest use them all. The 
reflections are too valuable to throw away. If data beyond some resolution is 
weak then they will have low contribution to the structure. Best if you 
calculate electron density maps at different resolutions at the end of 
refinement, compare them and use resolution that makes difference.



Regards,

Vaheh
8-5851

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
Koromyslova, Anna
Sent: Tuesday, July 11, 2017 12:32 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Problem with a cell content

Dear CCP4 members,

I am working on a structure of a protein in complex with an antibody fragment 
(approx. 50kDa together). Molecular replacement with closely related proteins 
always comes up with one complex in the asymmetric unit, although MW of protein 
to which Matthews applies is 125kDa and corresponds to two complexes.
Phaser gives two warnings:
Large non-origin Patterson peak indicates that translational NCS is present.
Solutions with Z-scores greater than 27.2 (the threshold indicating a definite 
solution) were rejected for failing packing test

I couldn’t get a solution with two subunits although I have tried multiple 
combinations including only conserved parts of both proteins and different 
space groups including P1. Phenix Autobuild also yielded only one complex.

So, the question is whether I can use that structure as is despite very high 
solvent content (80%) or should I try smth else. I would be very grateful for 
any suggestions.

When the solution with a single complex is refined the statistics are the 
following:

R-work  0.2129
R-free  0.2459
Matthews Coefficient: 6.22
Percentage Solvent: 80.22
Resolution range (Å)  48.34  - 2.9 (2.98  - 2.9)
Space group P 62 2 2
Unit cell  167.45 167.45 143.538 90 90 120
Multiplicity  19.1 (18.3)
Completeness (%)99.44 (94.39)
Mean I/sigma(I) 24.59 (2.71)
Wilson B-factor64.28
R-merge   0.1256 (1.186)
R-meas   0.1291
CC1/2 0.999 (0.85)
CC*1 (0.959)

Thank you very much for your help,

Anna


Dr. Anna Koromyslova, Postdoctoral researcher
German Cancer Research Center (DKFZ), F150
Im Neuenheimer Feld 242
D-69120 Heidelberg
Germany

To the extent this electronic communication or any of its attachments contain 
information that is not in the public domain, such information is considered by 
MedImmune to be confidential and proprietary. This communication is expected to 
be read and/or used only by the individual(s) for whom it is intended. If you 
have received this electronic communication in error, please reply to the 
sender advising of the error in transmission and delete the original message 
and any accompanying documents from your system immediately, 

Re: [ccp4bb] Problem with a cell content

[Koromyslova, Anna]

Dear Vaheh and Phil,

Sorry, I was a bit misleading – antibody fragment I used is a nanobody (VHH, 
15kDa). I was worried about the cell content because when I started the pdb 
deposition, there was a warning that solvent content is expected to be below 
80%, so I thought maybe I missed a correct solution. But if that’s acceptable 
value the problem is solved.
Thank you for the quick answer and the suggestion about the resolution!

Best regards,

Anna

Dr. Anna Koromyslova, Postdoctoral researcher
German Cancer Research Center (DKFZ), F150
Im Neuenheimer Feld 242
D-69120 Heidelberg
Germany


From: CCP4 bulletin board  on behalf of "Oganesyan, 
Vaheh" 
Reply-To: "Oganesyan, Vaheh" 
Date: Tuesday, July 11, 2017 at 7:05 PM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: [ccp4bb] Problem with a cell content

Похоже, что вы уже решили структуру. Почему вас беспокоит плотность ваших 
кристаллов? Кристаллы бывают разные.

First of all Fab by itself is already almost 50 kDa, so complex with antigen 
should be more than 50 kDa. Because you already solved the structure calculate 
the molecular mass based on your pdb file and rerun Matthews with correct mass. 
New numbers may be quite a bit different. Good indication of relatively low 
crystal density and consequently loose packing is the resolution of your data 
set. If you did not throw away data beyond 2.9A I’d suggest use them all. The 
reflections are too valuable to throw away. If data beyond some resolution is 
weak then they will have low contribution to the structure. Best if you 
calculate electron density maps at different resolutions at the end of 
refinement, compare them and use resolution that makes difference.



Regards,

Vaheh
8-5851

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
Koromyslova, Anna
Sent: Tuesday, July 11, 2017 12:32 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Problem with a cell content

Dear CCP4 members,

I am working on a structure of a protein in complex with an antibody fragment 
(approx. 50kDa together). Molecular replacement with closely related proteins 
always comes up with one complex in the asymmetric unit, although MW of protein 
to which Matthews applies is 125kDa and corresponds to two complexes.
Phaser gives two warnings:
Large non-origin Patterson peak indicates that translational NCS is present.
Solutions with Z-scores greater than 27.2 (the threshold indicating a definite 
solution) were rejected for failing packing test

I couldn’t get a solution with two subunits although I have tried multiple 
combinations including only conserved parts of both proteins and different 
space groups including P1. Phenix Autobuild also yielded only one complex.

So, the question is whether I can use that structure as is despite very high 
solvent content (80%) or should I try smth else. I would be very grateful for 
any suggestions.

When the solution with a single complex is refined the statistics are the 
following:

R-work  0.2129
R-free  0.2459
Matthews Coefficient: 6.22
Percentage Solvent: 80.22
Resolution range (Å)  48.34  - 2.9 (2.98  - 2.9)
Space group P 62 2 2
Unit cell  167.45 167.45 143.538 90 90 120
Multiplicity  19.1 (18.3)
Completeness (%)99.44 (94.39)
Mean I/sigma(I) 24.59 (2.71)
Wilson B-factor64.28
R-merge   0.1256 (1.186)
R-meas   0.1291
CC1/2 0.999 (0.85)
CC*1 (0.959)

Thank you very much for your help,

Anna


Dr. Anna Koromyslova, Postdoctoral researcher
German Cancer Research Center (DKFZ), F150
Im Neuenheimer Feld 242
D-69120 Heidelberg
Germany

To the extent this electronic communication or any of its attachments contain 
information that is not in the public domain, such information is considered by 
MedImmune to be confidential and proprietary. This communication is expected to 
be read and/or used only by the individual(s) for whom it is intended. If you 
have received this electronic communication in error, please reply to the 
sender advising of the error in transmission and delete the original message 
and any accompanying documents from your system immediately, without copying, 
reviewing or otherwise using them for any purpose. Thank you for your 
cooperation.

Re: [ccp4bb] Problem with a cell content

[Eleanor Dodson]

This is very strange . If you have a large non- crystallographic
translation vector you would expect either to have two molecules in the
asymmetric unit or your one molecule must have two very similar domains?
What is the n-c translation vector?

Could you have assigned too high symmetry ? SG maybe P 62? That could
explain the packing clashes Z scores of 27 are pretty good.

Eleanor


On 11 July 2017 at 18:05, Oganesyan, Vaheh  wrote:

> Похоже, что вы уже решили структуру. Почему вас беспокоит плотность ваших
> кристаллов? Кристаллы бывают разные.
>
>
>
> First of all Fab by itself is already almost 50 kDa, so complex with
> antigen should be more than 50 kDa. Because you already solved the
> structure calculate the molecular mass based on your pdb file and rerun
> Matthews with correct mass. New numbers may be quite a bit different. Good
> indication of relatively low crystal density and consequently loose packing
> is the resolution of your data set. If you did not throw away data beyond
> 2.9A I’d suggest use them all. The reflections are too valuable to throw
> away. If data beyond some resolution is weak then they will have low
> contribution to the structure. Best if you calculate electron density maps
> at different resolutions at the end of refinement, compare them and use
> resolution that makes difference.
>
>
>
>
>
>
>
> *Regards,*
>
>
>
> *Vaheh*
>
> *8-5851*
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of 
> *Koromyslova,
> Anna
> *Sent:* Tuesday, July 11, 2017 12:32 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Problem with a cell content
>
>
>
> Dear CCP4 members,
>
>
>
> I am working on a structure of a protein in complex with an antibody
> fragment (approx. 50kDa together). Molecular replacement with closely
> related proteins always comes up with one complex in the asymmetric unit,
> although MW of protein to which Matthews applies is 125kDa and corresponds
> to two complexes.
>
> Phaser gives two warnings:
>
> Large non-origin Patterson peak indicates that translational NCS is
> present.
>
> Solutions with Z-scores greater than 27.2 (the threshold indicating a
> definite solution) were rejected for failing packing test
>
>
>
> I couldn’t get a solution with two subunits although I have tried multiple
> combinations including only conserved parts of both proteins and different
> space groups including P1. Phenix Autobuild also yielded only one complex.
>
>
>
> So, the question is whether I can use that structure as is despite very
> high solvent content (80%) or should I try smth else. I would be very
> grateful for any suggestions.
>
>
>
> When the solution with a single complex is refined the statistics are the
> following:
>
>
>
> R-work  0.2129
>
> R-free  0.2459
>
> Matthews Coefficient: 6.22
>
> Percentage Solvent: 80.22
>
> Resolution range (Å)  48.34  - 2.9 (2.98  - 2.9)
>
> Space group P 62 2 2
>
> Unit cell  167.45 167.45 143.538 90 90 120
>
> Multiplicity  19.1 (18.3)
>
> Completeness (%)99.44 (94.39)
>
> Mean I/sigma(I) 24.59 (2.71)
>
> Wilson B-factor64.28
>
> R-merge   0.1256 (1.186)
>
> R-meas   0.1291
>
> CC1/2 0.999 (0.85)
>
> CC*1 (0.959)
>
>
>
> Thank you very much for your help,
>
>
>
> Anna
>
>
>
>
>
> Dr. Anna Koromyslova, Postdoctoral researcher
>
> German Cancer Research Center (DKFZ), F150
>
> Im Neuenheimer Feld 242
>
> D-69120 Heidelberg
>
> Germany
>
>
> To the extent this electronic communication or any of its attachments
> contain information that is not in the public domain, such information is
> considered by MedImmune to be confidential and proprietary. This
> communication is expected to be read and/or used only by the individual(s)
> for whom it is intended. If you have received this electronic communication
> in error, please reply to the sender advising of the error in transmission
> and delete the original message and any accompanying documents from your
> system immediately, without copying, reviewing or otherwise using them for
> any purpose. Thank you for your cooperation.
>

Re: [ccp4bb] Problem with a cell content

[Oganesyan, Vaheh]

Похоже, что вы уже решили структуру. Почему вас беспокоит плотность ваших 
кристаллов? Кристаллы бывают разные.

First of all Fab by itself is already almost 50 kDa, so complex with antigen 
should be more than 50 kDa. Because you already solved the structure calculate 
the molecular mass based on your pdb file and rerun Matthews with correct mass. 
New numbers may be quite a bit different. Good indication of relatively low 
crystal density and consequently loose packing is the resolution of your data 
set. If you did not throw away data beyond 2.9A I’d suggest use them all. The 
reflections are too valuable to throw away. If data beyond some resolution is 
weak then they will have low contribution to the structure. Best if you 
calculate electron density maps at different resolutions at the end of 
refinement, compare them and use resolution that makes difference.



Regards,

Vaheh
8-5851

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
Koromyslova, Anna
Sent: Tuesday, July 11, 2017 12:32 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Problem with a cell content

Dear CCP4 members,

I am working on a structure of a protein in complex with an antibody fragment 
(approx. 50kDa together). Molecular replacement with closely related proteins 
always comes up with one complex in the asymmetric unit, although MW of protein 
to which Matthews applies is 125kDa and corresponds to two complexes.
Phaser gives two warnings:
Large non-origin Patterson peak indicates that translational NCS is present.
Solutions with Z-scores greater than 27.2 (the threshold indicating a definite 
solution) were rejected for failing packing test

I couldn’t get a solution with two subunits although I have tried multiple 
combinations including only conserved parts of both proteins and different 
space groups including P1. Phenix Autobuild also yielded only one complex.

So, the question is whether I can use that structure as is despite very high 
solvent content (80%) or should I try smth else. I would be very grateful for 
any suggestions.

When the solution with a single complex is refined the statistics are the 
following:

R-work  0.2129
R-free  0.2459
Matthews Coefficient: 6.22
Percentage Solvent: 80.22
Resolution range (Å)  48.34  - 2.9 (2.98  - 2.9)
Space group P 62 2 2
Unit cell  167.45 167.45 143.538 90 90 120
Multiplicity  19.1 (18.3)
Completeness (%)99.44 (94.39)
Mean I/sigma(I) 24.59 (2.71)
Wilson B-factor64.28
R-merge   0.1256 (1.186)
R-meas   0.1291
CC1/2 0.999 (0.85)
CC*1 (0.959)

Thank you very much for your help,

Anna


Dr. Anna Koromyslova, Postdoctoral researcher
German Cancer Research Center (DKFZ), F150
Im Neuenheimer Feld 242
D-69120 Heidelberg
Germany

To the extent this electronic communication or any of its attachments contain 
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cooperation.

Re: [ccp4bb] Problem with a cell content

[Phil Jeffrey]

Hello Anna

You've already found the correct number of molecules in the asymmetric 
unit.  21% Rwork is a quite respectable value for a structure at this 
resolution, and while 80% solvent is a relatively rare occurrence it's 
not unprecedented (a couple of years back I did one at 3.0Å with 75% 
solvent - PDB 4U6U).  If you were missing half your asymmetric unit from 
your model, Rwork would be held up in the mid-30% range and there would 
be regions of relatively high difference density outside the model.


Phil Jeffrey
Princeton


On 7/11/17 12:31 PM, Koromyslova, Anna wrote:

Dear CCP4 members,

I am working on a structure of a protein in complex with an antibody 
fragment (approx. 50kDa together). Molecular replacement with closely 
related proteins always comes up with one complex in the asymmetric 
unit, although MW of protein to which Matthews applies is 125kDa and 
corresponds to two complexes.


Phaser gives two warnings:

Large non-origin Patterson peak indicates that translational NCS is present.

Solutions with Z-scores greater than 27.2 (the threshold indicating a 
definite solution) were rejected for failing packing test


I couldn’t get a solution with two subunits although I have tried 
multiple combinations including only conserved parts of both proteins 
and different space groups including P1. Phenix Autobuild also yielded 
only one complex.


So, the question is whether I can use that structure as is despite very 
high solvent content (80%) or should I try smth else. I would be very 
grateful for any suggestions.


When the solution with a single complex is refined the statistics are 
the following:


R-work  0.2129
R-free  0.2459
Matthews Coefficient: 6.22
Percentage Solvent: 80.22
Resolution range (Å)  48.34  - 2.9 (2.98  - 2.9)
Space group P 62 2 2
Unit cell  167.45 167.45 143.538 90 90 120
Multiplicity  19.1 (18.3)
Completeness (%)99.44 (94.39)
Mean I/sigma(I) 24.59 (2.71)
Wilson B-factor64.28
R-merge   0.1256 (1.186)
R-meas   0.1291
CC1/2 0.999 (0.85)
CC*1 (0.959)

Thank you very much for your help,

Anna
Dr. Anna Koromyslova, Postdoctoral researcher
German Cancer Research Center (DKFZ), F150
Im Neuenheimer Feld 242
D-69120 Heidelberg
Germany

[ccp4bb] Problem with a cell content

[Koromyslova, Anna]

Dear CCP4 members,

I am working on a structure of a protein in complex with an antibody fragment 
(approx. 50kDa together). Molecular replacement with closely related proteins 
always comes up with one complex in the asymmetric unit, although MW of protein 
to which Matthews applies is 125kDa and corresponds to two complexes.
Phaser gives two warnings:
Large non-origin Patterson peak indicates that translational NCS is present.
Solutions with Z-scores greater than 27.2 (the threshold indicating a definite 
solution) were rejected for failing packing test

I couldn’t get a solution with two subunits although I have tried multiple 
combinations including only conserved parts of both proteins and different 
space groups including P1. Phenix Autobuild also yielded only one complex.

So, the question is whether I can use that structure as is despite very high 
solvent content (80%) or should I try smth else. I would be very grateful for 
any suggestions.

When the solution with a single complex is refined the statistics are the 
following:

R-work  0.2129
R-free  0.2459
Matthews Coefficient: 6.22
Percentage Solvent: 80.22
Resolution range (Å)  48.34  - 2.9 (2.98  - 2.9)
Space group P 62 2 2
Unit cell  167.45 167.45 143.538 90 90 120
Multiplicity  19.1 (18.3)
Completeness (%)99.44 (94.39)
Mean I/sigma(I) 24.59 (2.71)
Wilson B-factor64.28
R-merge   0.1256 (1.186)
R-meas   0.1291
CC1/2 0.999 (0.85)
CC*1 (0.959)

Thank you very much for your help,

Anna


Dr. Anna Koromyslova, Postdoctoral researcher
German Cancer Research Center (DKFZ), F150
Im Neuenheimer Feld 242
D-69120 Heidelberg
Germany

[ccp4bb] AW: [ccp4bb] Inquiry - active and non-active state in alternatives

[Hughes, Jon]

dear petr,
several phytochrome structures seem to represent mixed-state crystals.
best,
jon

-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Petr 
Kolenko
Gesendet: Dienstag, 11. Juli 2017 16:00
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Inquiry - active and non-active state in alternatives

Dear colleagues,

We are working on a paper, where we want to discuss our crystal structure. We 
have determined structure of non-active state first (much easier). Than we 
tried to convert the protein into active state by soaking (direct 
crystallization not possible). We have observed more than a half of a protein 
chain in shifted location after soaking with respect to the original 
conformation as a 50% alternative. We believe that the alternative conformation 
corresponds to the active state and we are looking for any other possible 
support to our statement.

My questions are:
Has anyone else observed active and non-active state of a protein in single 
chain together as alternatives?
Has anyone an idea how to search through the PDB for such cases? Simple going 
through all structures with alternatives does not seem to be reasonable.

By the way, we are sure with the space group. Soaking may in some cases cause 
symmetry reduction, but if we process the data in lower symmetry, we see two 
chains with alternatives instead of one and this was not the only reason for 
our decision about the space group. We have also performed much more soaking 
experiments, but because of overall difficulty and instability of the 
chemicals, this was the best observation we ever had.

Thanks for any suggestion!
Best regards,
Petr

[ccp4bb] Inquiry - active and non-active state in alternatives

[Petr Kolenko]

Dear colleagues,

We are working on a paper, where we want to discuss our crystal 
structure. We have determined structure of non-active state first (much 
easier). Than we tried to convert the protein into active state by 
soaking (direct crystallization not possible). We have observed more 
than a half of a protein chain in shifted location after soaking with 
respect to the original conformation as a 50% alternative. We believe 
that the alternative conformation corresponds to the active state and we 
are looking for any other possible support to our statement.


My questions are:
Has anyone else observed active and non-active state of a protein in 
single chain together as alternatives?
Has anyone an idea how to search through the PDB for such cases? Simple 
going through all structures with alternatives does not seem to be 
reasonable.


By the way, we are sure with the space group. Soaking may in some cases 
cause symmetry reduction, but if we process the data in lower symmetry, 
we see two chains with alternatives instead of one and this was not the 
only reason for our decision about the space group. We have also 
performed much more soaking experiments, but because of overall 
difficulty and instability of the chemicals, this was the best 
observation we ever had.


Thanks for any suggestion!
Best regards,
Petr

[ccp4bb] Postdoctoral position in cryo-EM, Harvard Medical School

[Brown, Alan]

Dear all,

The Brown lab at Harvard Medical School has an opening for a postdoctoral 
scientist.

The lab uses the latest developments in cryo-EM to understand biological 
processes at the molecular level (e.g. Nature 524, 493–496 and Science 346, 
718–722). The project will involve investigating the structure and function of 
large macromolecular complexes involved in cellular transport. This includes 
all steps from construct design to structure determination. In the long term, 
we aim to use detailed molecular models to facilitate the development of new 
and better therapeutics.

Applicants should hold (or will be shortly awarded) a PhD degree and have 
experience in molecular biology and protein purification. Prior experience with 
single-particle cryo-EM or X-ray crystallography is considered a major 
advantage. Candidates should have strong communication skills and an 
established record of creativity through principal authorship in peer-reviewed 
publication(s). The successful candidate should be passionate about science, 
motivated, proactive, and able to work in a team. While each lab member has 
their own project, lab members are encouraged to work together to solve common 
problems. A separate position is available for an outstanding candidate with 
expertise in electron cryotomography (cryo-ET).

If you’re interested in joining the lab, please send your CV with a brief 
description of your current research as well as 2-3 contacts for references to 
alan_br...@hms.harvard.edu before the 8th 
August 2017.

For additional information about the job please visit our webpage: 
https://brown.hms.harvard.edu/

Best wishes,

Alan

Re: [ccp4bb] SHELXE: peptide occupancy refined to negative value

[Tim Gruene]

Dear Andreas,

did you try the option '-t' to make SHELXE try harder, or other building 
related options (take a look at the SHELX web page for talks and 
presentations).

Can you make use of the phases without model building? (sfall)

Since you seem to get a PDB-file, could you use the coordinates to calculate 
the phases off it? You can also provide the PDB-file as input file and restart 
phasing.

Best,
Tim

On Monday, July 10, 2017 5:51:57 PM CEST Andreas Förster wrote:
> Dear all,
> 
> since SHELX is now part of CCP4, this question is not entirely off-topic.
> 
> I'm trying to solve structures by S-SAD.  Substructure looks weak but ok if
> the right resolution cutoff is picked in SHELXD.
> 
> SHELXE is happy to do its thing for a while but then gives up with a
> "Peptide occupancy has refined to negative value" error in one hand.  The
> other hand is quite obviously (CC for partial structure, number of residues
> built) wrong, but the PDB obtained with the antimatter peptides looks like
> protein, is 80% complete and quite obviously the right solution.
> 
> Because of the error, SHELXE doesn't write phases.  How do I get these?  (I
> could do MR, but there must be a more elegant way...)  Better yet, what
> might cause the "negative occupancy" error and how do I avoid it?
> 
> Thanks and all best.
> 
> 
> Andreas
-- 
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
Principal Investigator
Biology and Chemistry
OFLC/104
CH-5232 Villigen PSI

Phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A



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Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

[Vellieux Frédéric]

Hello again,

Back in 2001 people still remembered the difference between Rsym and Rmerge. 16 
years later people seem to have forgotten. I will try to dig even more ancient 
references… Archaeology is the name of the game.

http://www.ysbl.york.ac.uk/ccp4bb/2001/msg00383.html

Cheers,

Fred.

From: James Foadi [mailto:james_fo...@yahoo.co.uk]
Sent: Tuesday, July 11, 2017 10:03 AM
To: Vellieux Frédéric ; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

Hello Frederic. Interesting. Have you got some reference on this to share?

James

Dr James Foadi PhD Diamond Light Source Ltd. Diamond House Harwell Science and 
Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: 
james.fo...@diamond.ac.uk alternative email: 
j.fo...@imperial.ac.uk personal web page: 
http://www.jfoadi.me.uk

On Tuesday, 11 July 2017, 7:15, Vellieux Frédéric 
> wrote:

Hello,

I think this needs a little bit of crystarchaeology.

Rmerge and Rsym used to be different. This was at a time when data sets were 
typically collected from several crystals. Pre-cryo cooling, with data recorded 
on photographic film (Arndt-Wonacott cameras).

Rmerge = agreement R-factor from data from several crystals;
Rsym = agreement R-factor from symmetry-equivalents within one crystal.

[I just type "agreement R-factor" in order not to have to type the formulae]

At that time, people were confused about these two terms.

Nowadays both are (used as) synonyms.

Cheers,

Fred.

-Original Message-
From: CCP4 bulletin board 
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phil 
Evans
Sent: Monday, July 10, 2017 5:43 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

What is the difference between Rmerge and Rsym - I thought they were the same?
Rrim == Rmeas I think

Phil



> On 10 Jul 2017, at 15:18, John Berrisford 
> > wrote:
>
> Dear Herman
>
> The new PDB deposition system (OneDep) allows you to enter values for Rmerge, 
> Rsym, Rpim, Rrim and / or CC half. If, during deposition, you do not provide 
> a value for any of these metrics then we will ask you for a value for one of 
> them.
>
> Also, PDB format is a legacy format for the PDB. In 2014 mmCIF became the 
> archive format for the PDB and some large entries are no longer distributed 
> in PDB format. mmCIF is not limited by the constraints of punch cards.
>
> Please see
> https://www.wwpdb.org/documentation/file-formats-and-the-pdb
>
> Regards
>
> John
>
> PDBe
>
>
>
> On 10/07/2017 09:26, 
> herman.schreu...@sanofi.com wrote:
>> Dear All,
>>
>> For me this whole discussion is an example of a large number of people 
>> barking at the wrong tree. The real issue is not whether data processing 
>> programs print amongst many quality indicators an Rmerge as well, but the 
>> fact that the PDB and many journals still insist on using the Rmerge as 
>> primary quality indicator. As long as this is true, novice scientist might 
>> be led to believe that Rmerge is the most important quality indicator. As 
>> soon as the PDB and the journals request some other indicator, this will be 
>> over. So that is where we should direct our efforts to.
>>
>> I don't understand at all, why the PDB still insists on an obsolete quality 
>> indicator. However, the PDB format for the coordinates also dates back to 
>> the 1960's to be used with punch cards.
>>
>> My 2 cents.
>> Herman
>>
>>
>>
>> -Ursprüngliche Nachricht-
>> Von: CCP4 bulletin board 
>> [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag
>> von Edward A. Berry
>> Gesendet: Samstag, 8. Juli 2017 22:31
>> An: CCP4BB@JISCMAIL.AC.UK
>> Betreff: Re: [ccp4bb] Rmergicide Through Programming
>>
>> But R-merge is not really narrower as a fraction of the mean value- it just 
>> gets smaller proportionantly as all the numbers get smaller:
>> RMSD of .0043 for R-meas multiplied by factor of 0.022/.027 gives 0.0035 
>> which is the RMSD for Rmerge. The same was true in the previous example. You 
>> could multiply R-meas by .5 or .2 and get a sharper distribution yet! And 
>> that factor would be constant, where this only applies for super-low 
>> redundancy.
>>
>> On 07/08/2017 03:23 PM, James Holton wrote:
>>> The expected distribution of Rmeas values is still wider than that of 
>>> Rmerge for data with I/sigma=30 and average multiplicity=2.0. Graph 
>>> attached.
>>>
>>> I expect that anytime you incorporate more than one source of information 
>>> you run the risk of a noisier statistic because every source of information 
>>> can contain noise.  That is, Rmeas combines information about multiplicity 
>>> with the 

Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

[James Foadi]

Hello Frederic. Interesting. Have you got some reference on this to share?
James
 Dr James Foadi PhD Diamond Light Source Ltd. Diamond House Harwell Science and 
Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: 
james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk personal 
web page: http://www.jfoadi.me.uk 

On Tuesday, 11 July 2017, 7:15, Vellieux Frédéric 
 wrote:
 

 Hello,

I think this needs a little bit of crystarchaeology.

Rmerge and Rsym used to be different. This was at a time when data sets were 
typically collected from several crystals. Pre-cryo cooling, with data recorded 
on photographic film (Arndt-Wonacott cameras).

Rmerge = agreement R-factor from data from several crystals;
Rsym = agreement R-factor from symmetry-equivalents within one crystal.

[I just type "agreement R-factor" in order not to have to type the formulae]

At that time, people were confused about these two terms.

Nowadays both are (used as) synonyms.

Cheers,

Fred.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phil Evans
Sent: Monday, July 10, 2017 5:43 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

What is the difference between Rmerge and Rsym - I thought they were the same?
Rrim == Rmeas I think

Phil



> On 10 Jul 2017, at 15:18, John Berrisford  wrote:
>
> Dear Herman
>
> The new PDB deposition system (OneDep) allows you to enter values for Rmerge, 
> Rsym, Rpim, Rrim and / or CC half. If, during deposition, you do not provide 
> a value for any of these metrics then we will ask you for a value for one of 
> them.
>
> Also, PDB format is a legacy format for the PDB. In 2014 mmCIF became the 
> archive format for the PDB and some large entries are no longer distributed 
> in PDB format. mmCIF is not limited by the constraints of punch cards.
>
> Please see
> https://www.wwpdb.org/documentation/file-formats-and-the-pdb
>
> Regards
>
> John
>
> PDBe
>
>
>
> On 10/07/2017 09:26, herman.schreu...@sanofi.com wrote:
>> Dear All,
>>
>> For me this whole discussion is an example of a large number of people 
>> barking at the wrong tree. The real issue is not whether data processing 
>> programs print amongst many quality indicators an Rmerge as well, but the 
>> fact that the PDB and many journals still insist on using the Rmerge as 
>> primary quality indicator. As long as this is true, novice scientist might 
>> be led to believe that Rmerge is the most important quality indicator. As 
>> soon as the PDB and the journals request some other indicator, this will be 
>> over. So that is where we should direct our efforts to.
>>
>> I don't understand at all, why the PDB still insists on an obsolete quality 
>> indicator. However, the PDB format for the coordinates also dates back to 
>> the 1960's to be used with punch cards.
>>
>> My 2 cents.
>> Herman
>>
>>
>>
>> -Ursprüngliche Nachricht-
>> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag
>> von Edward A. Berry
>> Gesendet: Samstag, 8. Juli 2017 22:31
>> An: CCP4BB@JISCMAIL.AC.UK
>> Betreff: Re: [ccp4bb] Rmergicide Through Programming
>>
>> But R-merge is not really narrower as a fraction of the mean value- it just 
>> gets smaller proportionantly as all the numbers get smaller:
>> RMSD of .0043 for R-meas multiplied by factor of 0.022/.027 gives 0.0035 
>> which is the RMSD for Rmerge. The same was true in the previous example. You 
>> could multiply R-meas by .5 or .2 and get a sharper distribution yet! And 
>> that factor would be constant, where this only applies for super-low 
>> redundancy.
>>
>> On 07/08/2017 03:23 PM, James Holton wrote:
>>> The expected distribution of Rmeas values is still wider than that of 
>>> Rmerge for data with I/sigma=30 and average multiplicity=2.0. Graph 
>>> attached.
>>>
>>> I expect that anytime you incorporate more than one source of information 
>>> you run the risk of a noisier statistic because every source of information 
>>> can contain noise.  That is, Rmeas combines information about multiplicity 
>>> with the absolute deviates in the data to form a statistic that is more 
>>> accurate that Rmerge, but also (potentially) less precise.
>>>
>>> Perhaps that is what we are debating here?  Which is better? accuracy or 
>>> precision?  Personally, I prefer to know both.
>>>
>>> -James Holton
>>> MAD Scientist
>>>
>>> On 7/8/2017 11:02 AM, Frank von Delft wrote:
 It is quite easy to end up with low multiplicities in the low resolution 
 shell, especially for low symmetry and fast-decaying crystals.

 It is this scenario where Rmerge (lowres) is more misleading than Reas.

 phx


 On 08/07/2017 17:31, James Holton wrote:
> What does Rmeas tell us that Rmerge doesn't?  Given that we know the 
> multiplicity?
>
> -James Holton
> MAD Scientist
>
> On 

Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

[Vellieux Frédéric]

Hello,

I think this needs a little bit of crystarchaeology.

Rmerge and Rsym used to be different. This was at a time when data sets were 
typically collected from several crystals. Pre-cryo cooling, with data recorded 
on photographic film (Arndt-Wonacott cameras).

Rmerge = agreement R-factor from data from several crystals;
Rsym = agreement R-factor from symmetry-equivalents within one crystal.

[I just type "agreement R-factor" in order not to have to type the formulae]

At that time, people were confused about these two terms.

Nowadays both are (used as) synonyms.

Cheers,

Fred.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phil Evans
Sent: Monday, July 10, 2017 5:43 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

What is the difference between Rmerge and Rsym - I thought they were the same?
Rrim == Rmeas I think

Phil



> On 10 Jul 2017, at 15:18, John Berrisford  wrote:
>
> Dear Herman
>
> The new PDB deposition system (OneDep) allows you to enter values for Rmerge, 
> Rsym, Rpim, Rrim and / or CC half. If, during deposition, you do not provide 
> a value for any of these metrics then we will ask you for a value for one of 
> them.
>
> Also, PDB format is a legacy format for the PDB. In 2014 mmCIF became the 
> archive format for the PDB and some large entries are no longer distributed 
> in PDB format. mmCIF is not limited by the constraints of punch cards.
>
> Please see
> https://www.wwpdb.org/documentation/file-formats-and-the-pdb
>
> Regards
>
> John
>
> PDBe
>
>
>
> On 10/07/2017 09:26, herman.schreu...@sanofi.com wrote:
>> Dear All,
>>
>> For me this whole discussion is an example of a large number of people 
>> barking at the wrong tree. The real issue is not whether data processing 
>> programs print amongst many quality indicators an Rmerge as well, but the 
>> fact that the PDB and many journals still insist on using the Rmerge as 
>> primary quality indicator. As long as this is true, novice scientist might 
>> be led to believe that Rmerge is the most important quality indicator. As 
>> soon as the PDB and the journals request some other indicator, this will be 
>> over. So that is where we should direct our efforts to.
>>
>> I don't understand at all, why the PDB still insists on an obsolete quality 
>> indicator. However, the PDB format for the coordinates also dates back to 
>> the 1960's to be used with punch cards.
>>
>> My 2 cents.
>> Herman
>>
>>
>>
>> -Ursprüngliche Nachricht-
>> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag
>> von Edward A. Berry
>> Gesendet: Samstag, 8. Juli 2017 22:31
>> An: CCP4BB@JISCMAIL.AC.UK
>> Betreff: Re: [ccp4bb] Rmergicide Through Programming
>>
>> But R-merge is not really narrower as a fraction of the mean value- it just 
>> gets smaller proportionantly as all the numbers get smaller:
>> RMSD of .0043 for R-meas multiplied by factor of 0.022/.027 gives 0.0035 
>> which is the RMSD for Rmerge. The same was true in the previous example. You 
>> could multiply R-meas by .5 or .2 and get a sharper distribution yet! And 
>> that factor would be constant, where this only applies for super-low 
>> redundancy.
>>
>> On 07/08/2017 03:23 PM, James Holton wrote:
>>> The expected distribution of Rmeas values is still wider than that of 
>>> Rmerge for data with I/sigma=30 and average multiplicity=2.0. Graph 
>>> attached.
>>>
>>> I expect that anytime you incorporate more than one source of information 
>>> you run the risk of a noisier statistic because every source of information 
>>> can contain noise.  That is, Rmeas combines information about multiplicity 
>>> with the absolute deviates in the data to form a statistic that is more 
>>> accurate that Rmerge, but also (potentially) less precise.
>>>
>>> Perhaps that is what we are debating here?  Which is better? accuracy or 
>>> precision?  Personally, I prefer to know both.
>>>
>>> -James Holton
>>> MAD Scientist
>>>
>>> On 7/8/2017 11:02 AM, Frank von Delft wrote:
 It is quite easy to end up with low multiplicities in the low resolution 
 shell, especially for low symmetry and fast-decaying crystals.

 It is this scenario where Rmerge (lowres) is more misleading than Reas.

 phx


 On 08/07/2017 17:31, James Holton wrote:
> What does Rmeas tell us that Rmerge doesn't?  Given that we know the 
> multiplicity?
>
> -James Holton
> MAD Scientist
>
> On 7/8/2017 9:15 AM, Frank von Delft wrote:
>> Anyway, back to reality:  does anybody still use R statistics to 
>> evaluate anything other than /strong/ data?  Certainly I never look at 
>> it except for the low-resolution bin (or strongest reflections). 
>> Specifically, a "2%-dataset" in that bin is probably healthy, while a 
>> "9%-dataset" probably Has Issues.
>>
>> In which case, back to Jacob's question:  what does