Re: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports

[Pavel Afonine]

I find Lothar's comments regarding H and RSRZ excellent! I would think of
it as a pretty much bug report. I hope developers at that end listen. This
goes very well in line with Phoebe's comment earlier today.

Pavel

On Mon, Nov 28, 2016 at 2:51 PM, Dale Tronrud  wrote:

> On 11/28/2016 12:52 PM, esse...@helix.nih.gov wrote:
> >> I found that one can get RSRZ to go way down by loosening the geometry
> >> restraints.  The result is a crappy structure and I don't recommend
> doing
> >> that, but it does get all the atoms crammed into some sort of density.
> >
> >   Your observation is quite interesting. I can add this: when we were
> working
> > with low to medium resolution structures, deleting the hydrogen atoms
> from
> > the model after refinement moved the very bad RSRZ statistic to about the
> > average in the given resolution range! Note, no re-refinement was done
> just
> > a simple deletion of the riding H-atoms. I find this to be odd given the
> > fact that, say the phenix developers favor the inclusion of H-atoms on
> > riding positions even in cases of low resolution structures. (I assume
> the
> > refmac5 and BUSTER-TNT developers have also a favorable opinion about
> > including H-atoms in the final model - and during refinement).
> >
> > In my mind, it may be tempting to delete H-atoms to improve this
> statistic but
> > when you use them in refinement they should be included regardless of the
> > outcome of the RSRZ analysis.
>
>Of course, if you trick a validation statistic like this you haven't
> accomplished anything.  All you are saying is that one should rank RSRZ
> scores with and without hydrogen atoms separately.  Perhaps you should
> suggest that to the PDB validation people.
>
> Dale Tronrud
> >
> >>
> >> RSRZ, in my most humble of opinions, seems like one of those statistics
> that
> >> is far more useful in theory than reality.   Particularly for
> >> medium-resolution structures, the fit of each entire side chain to the
> density
> >> is likely to be imperfect because the density is imperfect, especially
> toward
> >> the tips of those side chains.
> >>
> >> Then again, it can be a good flag for bits of the structure worth a
> second
> >> look in rebuilding.
> >
> >   The latter is certainly true. It may mean that the developers of RSRZ
> > analysis need to tune it a bit to make it fully useful.
> >
> > L.
> >
> >>
> >> 
> >> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Matthew
> >> Bratkowski [mab...@cornell.edu]
> >> Sent: Tuesday, November 22, 2016 10:12 AM
> >> To: CCP4BB@JISCMAIL.AC.UK
> >> Subject: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports
> >>
> >> Hello all,
> >>
> >> I was wondering if anyone knew how the RSRZ score was calculated in the
> >> protein data bank validation reports and how useful of a metric this
> actually
> >> is for structure validation?  I am trying to improve this score on a
> structure
> >> that I am working on, but I'm not really sure where to begin.  From my
> >> understanding, the score is based on the number of RSRZ outliers with a
> score
> >>> 2.  In my case, I have several residues with scores between 2 and 4,
> but at
> >> least by eye, fit to the electron density does not look that bad.
> Hence, I
> >> can't justify deleting them to try to improve the score.  If the score
> is just
> >> based on percent of outlier residues, then for instance wouldn't a
> structure
> >> with say 20 residues modeled with no corresponding electron density
> have the
> >> same score as a structure with 20 residues with RSRZ values of say 2.5?
> >>
> >>
> >> I was also wondering how the resolution of the structure relates to the
> score?
> >>  Glancing through several pdb validation reports, I noticed some
> structure
> >> with low resolution (3.5 A or lower) with relatively high scores, while
> others
> >> with high resolution (2 A or higher) getting low scores.  It is
> reasonable to
> >> assume that a structure of lower than 3.5 A would be missing several
> side
> >> chains and may also have some ambiguous main chain electron density,
> which
> >> should in theory increase the RSRZ score.  While of course every
> structure is
> >> different and the quality of it due to the rigor of the person building
> the
> >> model, I was wondering if there were any general trends related to
> resolution
> >> and RSRZ score.
> >>
> >> Thanks,
> >> Matt
> >>
> >
>

Re: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports

[Dale Tronrud]

On 11/28/2016 12:52 PM, esse...@helix.nih.gov wrote:
>> I found that one can get RSRZ to go way down by loosening the geometry
>> restraints.  The result is a crappy structure and I don't recommend doing
>> that, but it does get all the atoms crammed into some sort of density.
> 
>   Your observation is quite interesting. I can add this: when we were working
> with low to medium resolution structures, deleting the hydrogen atoms from
> the model after refinement moved the very bad RSRZ statistic to about the
> average in the given resolution range! Note, no re-refinement was done just
> a simple deletion of the riding H-atoms. I find this to be odd given the
> fact that, say the phenix developers favor the inclusion of H-atoms on
> riding positions even in cases of low resolution structures. (I assume the
> refmac5 and BUSTER-TNT developers have also a favorable opinion about
> including H-atoms in the final model - and during refinement).
> 
> In my mind, it may be tempting to delete H-atoms to improve this statistic but
> when you use them in refinement they should be included regardless of the
> outcome of the RSRZ analysis.

   Of course, if you trick a validation statistic like this you haven't
accomplished anything.  All you are saying is that one should rank RSRZ
scores with and without hydrogen atoms separately.  Perhaps you should
suggest that to the PDB validation people.

Dale Tronrud
> 
>>
>> RSRZ, in my most humble of opinions, seems like one of those statistics that
>> is far more useful in theory than reality.   Particularly for
>> medium-resolution structures, the fit of each entire side chain to the 
>> density
>> is likely to be imperfect because the density is imperfect, especially toward
>> the tips of those side chains.
>>
>> Then again, it can be a good flag for bits of the structure worth a second
>> look in rebuilding.
> 
>   The latter is certainly true. It may mean that the developers of RSRZ
> analysis need to tune it a bit to make it fully useful.
> 
> L.
> 
>>
>> 
>> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Matthew
>> Bratkowski [mab...@cornell.edu]
>> Sent: Tuesday, November 22, 2016 10:12 AM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports
>>
>> Hello all,
>>
>> I was wondering if anyone knew how the RSRZ score was calculated in the
>> protein data bank validation reports and how useful of a metric this actually
>> is for structure validation?  I am trying to improve this score on a 
>> structure
>> that I am working on, but I'm not really sure where to begin.  From my
>> understanding, the score is based on the number of RSRZ outliers with a score
>>> 2.  In my case, I have several residues with scores between 2 and 4, but at
>> least by eye, fit to the electron density does not look that bad.  Hence, I
>> can't justify deleting them to try to improve the score.  If the score is 
>> just
>> based on percent of outlier residues, then for instance wouldn't a structure
>> with say 20 residues modeled with no corresponding electron density have the
>> same score as a structure with 20 residues with RSRZ values of say 2.5?
>>
>>
>> I was also wondering how the resolution of the structure relates to the 
>> score?
>>  Glancing through several pdb validation reports, I noticed some structure
>> with low resolution (3.5 A or lower) with relatively high scores, while 
>> others
>> with high resolution (2 A or higher) getting low scores.  It is reasonable to
>> assume that a structure of lower than 3.5 A would be missing several side
>> chains and may also have some ambiguous main chain electron density, which
>> should in theory increase the RSRZ score.  While of course every structure is
>> different and the quality of it due to the rigor of the person building the
>> model, I was wondering if there were any general trends related to resolution
>> and RSRZ score.
>>
>> Thanks,
>> Matt
>>
> 

[ccp4bb] sorry for spamming

[Alexandre OURJOUMTSEV]

Dear all,


sorry for spamming your mail boxes - there is a bug in our system.


Best regards,


Sacha

Re: [ccp4bb] wavelet application in CCP4

[Alexandre OURJOUMTSEV]

Dear Charles,


if you are interested in applications of wavelets to macromolecular 
crystallography problems, you may look also at a slightly earlier publication 
by Vladimir Lunin in


 Acta Cryst (2000) A56, 73-84

"Fixed-scale wavelet-type approximation of periodic density distributions."


Best regards,


Sacha Urzhumtsev




De : CCP4 bulletin board  de la part de CPMAS Chen 

Envoyé : lundi 28 novembre 2016 17:16
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] wavelet application in CCP4

Dear, All

I happen to see this paper,

Low-resolution phase extension using wavelet analysis.
Main 
P1,
 Wilson 
J

However, I did not see any application in current structure refinement 
softwares. Maybe I overlooked this function in CCP4/phenix etc?

Also, I did not see much references to this paper?

Could anyone give me some heads-up?

Thanks!

Charles

--

***

Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

**

Re: [ccp4bb] wavelet application in CCP4

[Alexandre OURJOUMTSEV]

Dear Charles,


if you are interested in applications of wavelets to macromolecular 
crystallography, you may look also at a slightly earlier publication by 
Vladimir Lunin


Acta Cryst. (2000). 
A56, 73-84
https://doi.org/10.1107/S0108767399011277
Fixed-scale wavelet-type approximation of periodic density 
distributions
V. Y. 
Lunin


Best regards,


Sacha Urzhumtsev



De : CCP4 bulletin board  de la part de CPMAS Chen 

Envoyé : lundi 28 novembre 2016 17:16
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] wavelet application in CCP4

Dear, All

I happen to see this paper,

Low-resolution phase extension using wavelet analysis.
Main 
P1,
 Wilson 
J

However, I did not see any application in current structure refinement 
softwares. Maybe I overlooked this function in CCP4/phenix etc?

Also, I did not see much references to this paper?

Could anyone give me some heads-up?

Thanks!

Charles

--

***

Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

**

Re: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports

[esserlo]

> I found that one can get RSRZ to go way down by loosening the geometry
> restraints.  The result is a crappy structure and I don't recommend doing
> that, but it does get all the atoms crammed into some sort of density.

  Your observation is quite interesting. I can add this: when we were working
with low to medium resolution structures, deleting the hydrogen atoms from
the model after refinement moved the very bad RSRZ statistic to about the
average in the given resolution range! Note, no re-refinement was done just
a simple deletion of the riding H-atoms. I find this to be odd given the
fact that, say the phenix developers favor the inclusion of H-atoms on
riding positions even in cases of low resolution structures. (I assume the
refmac5 and BUSTER-TNT developers have also a favorable opinion about
including H-atoms in the final model - and during refinement).

In my mind, it may be tempting to delete H-atoms to improve this statistic but
when you use them in refinement they should be included regardless of the
outcome of the RSRZ analysis.

>
> RSRZ, in my most humble of opinions, seems like one of those statistics that
> is far more useful in theory than reality.   Particularly for
> medium-resolution structures, the fit of each entire side chain to the density
> is likely to be imperfect because the density is imperfect, especially toward
> the tips of those side chains.
>
> Then again, it can be a good flag for bits of the structure worth a second
> look in rebuilding.

  The latter is certainly true. It may mean that the developers of RSRZ
analysis need to tune it a bit to make it fully useful.

L.

>
> 
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Matthew
> Bratkowski [mab...@cornell.edu]
> Sent: Tuesday, November 22, 2016 10:12 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports
>
> Hello all,
>
> I was wondering if anyone knew how the RSRZ score was calculated in the
> protein data bank validation reports and how useful of a metric this actually
> is for structure validation?  I am trying to improve this score on a structure
> that I am working on, but I'm not really sure where to begin.  From my
> understanding, the score is based on the number of RSRZ outliers with a score
> >2.  In my case, I have several residues with scores between 2 and 4, but at
> least by eye, fit to the electron density does not look that bad.  Hence, I
> can't justify deleting them to try to improve the score.  If the score is just
> based on percent of outlier residues, then for instance wouldn't a structure
> with say 20 residues modeled with no corresponding electron density have the
> same score as a structure with 20 residues with RSRZ values of say 2.5?
>
>
> I was also wondering how the resolution of the structure relates to the score?
>  Glancing through several pdb validation reports, I noticed some structure
> with low resolution (3.5 A or lower) with relatively high scores, while others
> with high resolution (2 A or higher) getting low scores.  It is reasonable to
> assume that a structure of lower than 3.5 A would be missing several side
> chains and may also have some ambiguous main chain electron density, which
> should in theory increase the RSRZ score.  While of course every structure is
> different and the quality of it due to the rigor of the person building the
> model, I was wondering if there were any general trends related to resolution
> and RSRZ score.
>
> Thanks,
> Matt
>

[ccp4bb] Need suggestions on Mac Pro and accessories for structural biology work

[yanfeng zhou]

Dear CCP4 community,

I am posting to get your suggestions on a Mac Pro system for structural
biology and not entertainment.  Any comments will be appreciated.  Please
feel free to send off line messages if you prefer.

My target is a Mac Pro with 8-12 cores and Dual AMD FirePro D700 GPUs. I
will run structural biology programs with light to intense computation
load, and 3D display of protein structures on a 24-27 inch monitor is a
necessity.  This system will be remotely connected to a cluster for time
consuming computation.

Here come the questions.
1. What will be a good monitor (brand, model, etc) for my setup?  What
specs should I pay attention when shopping for the monitor so I won't face
any compatibility or 3D display issue?
2. Suggestions of emitters and glasses paired with Mac Pro and monitor are
highly welcome. Or could I add an emitter on Mac Pro like on a Linux box?
3. There are many adapters and cables for Mac, so recommendations on
adapter selection to make a Mac Pro-3D monitor package will be greatly
appreciated too.
4. Anything I need to notice to have a complete ready-to-go system but is
missed in this email (excluding mouse, keyboard, and speakers).

Thank you for reading the post, and wish you a great start of the week.

Best,
Yanfeng

Re: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports

[Pavel Afonine]

On Mon, Nov 28, 2016 at 10:17 AM, Phoebe A. Rice  wrote:

> RSRZ, in my most humble of opinions, seems like one of those statistics
> that is far more useful in theory than reality.
>

Can't agree more!
Pavel

Re: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports

[Phoebe A. Rice]

I found that one can get RSRZ to go way down by loosening the geometry 
restraints.  The result is a crappy structure and I don't recommend doing that, 
but it does get all the atoms crammed into some sort of density.

RSRZ, in my most humble of opinions, seems like one of those statistics that is 
far more useful in theory than reality.   Particularly for medium-resolution 
structures, the fit of each entire side chain to the density is likely to be 
imperfect because the density is imperfect, especially toward the tips of those 
side chains.

Then again, it can be a good flag for bits of the structure worth a second look 
in rebuilding.


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Matthew 
Bratkowski [mab...@cornell.edu]
Sent: Tuesday, November 22, 2016 10:12 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports

Hello all,

I was wondering if anyone knew how the RSRZ score was calculated in the protein 
data bank validation reports and how useful of a metric this actually is for 
structure validation?  I am trying to improve this score on a structure that I 
am working on, but I'm not really sure where to begin.  From my understanding, 
the score is based on the number of RSRZ outliers with a score >2.  In my case, 
I have several residues with scores between 2 and 4, but at least by eye, fit 
to the electron density does not look that bad.  Hence, I can't justify 
deleting them to try to improve the score.  If the score is just based on 
percent of outlier residues, then for instance wouldn't a structure with say 20 
residues modeled with no corresponding electron density have the same score as 
a structure with 20 residues with RSRZ values of say 2.5?


I was also wondering how the resolution of the structure relates to the score?  
Glancing through several pdb validation reports, I noticed some structure with 
low resolution (3.5 A or lower) with relatively high scores, while others with 
high resolution (2 A or higher) getting low scores.  It is reasonable to assume 
that a structure of lower than 3.5 A would be missing several side chains and 
may also have some ambiguous main chain electron density, which should in 
theory increase the RSRZ score.  While of course every structure is different 
and the quality of it due to the rigor of the person building the model, I was 
wondering if there were any general trends related to resolution and RSRZ score.

Thanks,
Matt

Re: [ccp4bb] wavelet application in CCP4

[Alexandre OURJOUMTSEV]

Dear Charles,


if you are interested in applications of wavelets to macromolecular 
crystallography, you may look also at a slightly earlier publication by 
Vladimir Lunin


Acta Cryst. (2000). 
A56, 73-84
https://doi.org/10.1107/S0108767399011277
Fixed-scale wavelet-type approximation of periodic density 
distributions
V. Y. 
Lunin


Best regards,


Sacha Urzhumtsev



De : CCP4 bulletin board  de la part de CPMAS Chen 

Envoyé : lundi 28 novembre 2016 17:16
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] wavelet application in CCP4

Dear, All

I happen to see this paper,

Low-resolution phase extension using wavelet analysis.
Main 
P1,
 Wilson 
J

However, I did not see any application in current structure refinement 
softwares. Maybe I overlooked this function in CCP4/phenix etc?

Also, I did not see much references to this paper?

Could anyone give me some heads-up?

Thanks!

Charles

--

***

Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

**

Re: [ccp4bb] wavelet application in CCP4

[Harry Powell]

Hi

Phase extension, albeit at high (rather than low) resolution (and I don't think 
it uses wavelets) has been more recently popularised in the various 
implementations of the "free lunch algorithm". Otherwise that might be a good 
place to start looking.

Harry
--
Dr Harry Powell
Chairman of International Union of Crystallography Commission on 
Crystallographic Computing
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 

> On 28 Nov 2016, at 16:57, James Foadi 
> <09daa8ec3774-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Peter Main is retired. Julie works on different stuff now. I'm not aware of 
> any application aside what Julie implemented at the end of the 90s.
> 
> James
> 
> 
> Sent from Yahoo Mail for iPhone
> 
> On Monday, November 28, 2016, 4:16 pm, CPMAS Chen  wrote:
> 
> Dear, All
> 
> I happen to see this paper,
> 
> Low-resolution phase extension using wavelet analysis.
> Main P1, Wilson J
> 
> However, I did not see any application in current structure refinement 
> softwares. Maybe I overlooked this function in CCP4/phenix etc?
> 
> Also, I did not see much references to this paper?
> 
> Could anyone give me some heads-up?
> 
> Thanks!
> 
> Charles
> 
> -- 
> ***
> 
> Charles Chen
> 
> Research Associate
> 
> University of Pittsburgh School of Medicine
> 
> Department of Anesthesiology
> 
> **
> 

Re: [ccp4bb] wavelet application in CCP4

[James Foadi]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; } Peter Main is retired. Julie works on different stuff now. I'm 
not aware of any application aside what Julie implemented at the end of the 90s.
James


Sent from Yahoo Mail for iPhone


On Monday, November 28, 2016, 4:16 pm, CPMAS Chen  wrote:

Dear, All
I happen to see this paper,

Low-resolution phase extension using wavelet analysis.
Main P1, Wilson J
However, I did not see any application in current structure refinement 
softwares. Maybe I overlooked this function in CCP4/phenix etc?
Also, I did not see much references to this paper?
Could anyone give me some heads-up?
Thanks!
Charles
-- 



***

Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

**

[ccp4bb] wavelet application in CCP4

[CPMAS Chen]

Dear, All

I happen to see this paper,

Low-resolution phase extension using wavelet analysis.
Main P

1, Wilson J


However, I did not see any application in current structure refinement
softwares. Maybe I overlooked this function in CCP4/phenix etc?

Also, I did not see much references to this paper?

Could anyone give me some heads-up?

Thanks!

Charles

-- 

***

Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

**

Re: [ccp4bb] Density for an unknown ligand

[Tushar R.]

Dear Wei,
I am not sure which molecule this density corresponds to but I think you
should also consider the possibility of a molecule that can be fitted in
the density but is in fact at a special position meaning that the axis of
symmetry passes through the center of the molecule leading to presence
symmetry related molecule also in the same position. However, this would
obviously mean that the atoms of these two molecules would have partial
occupancies.

Best,
Tushar.

On Mon, Nov 28, 2016 at 5:27 PM, Bythell-Douglas, Rohan R <
r.bythell-doug...@imperial.ac.uk> wrote:

> Dear Wei,
>
> I think Prem’s suggestion that the molecule is on a symmetry axis is
> right. There are 2 images in those that you have sent that show a two fold
> rotation axis within the missing density, so I think the density
> corresponds to two molecules. - possibly something like PMSF? Did you
> happen to use PMSF during your purification?
>
> Regards,
> Rohan
>
> On 28 Nov 2016, at 11:36, Prem Prakash  wrote:
>
> Dear Wei,
> I am not sure but is it possible that the crystallization condition you
> have used has already this compound (may be as an impurity) rather than
> expecting this as an extract from E. coli. If that can be searched it may
> be useful.
>
> Good luck
> Have a nice day
>
> On Mon, Nov 28, 2016 at 3:51 PM, LiuWei  wrote:
>
>> Hi Prem,
>>
>> Thanks for your response. The compound really looks to be a two-fold
>> symmetry related molecule, but I am very sure that it is not located at a
>> symmetry axis. It looks like a compound with 3 or 4 terminal ring, could-be
>> two molecules of biphenyl enter. Such a compound, however, is almost
>> insoluble, and I wonder if it can be copurified with a protein.
>>
>> Regards
>> Wei
>>
>> 2016年11月28日 下午02:50，Prem Prakash  写道：
>>
>> Hi Wei,
>> Is the electron density of this compound lie at the symmetry axis ? It
>> seems to me that two planar rings with one connecting oxygen. And the
>> compound is more looks like a diphenyl ether to me with its symmetry
>> related molecule.
>>
>> Hope others will give some more idea about it.
>>
>> Cheers
>> P.P
>>
>> On Sun, Nov 27, 2016 at 4:03 PM, Wei Liu  wrote:
>>
>>> Dear all,
>>>
>>> We have recently crystallized a recombinant protein produce from E.
>>> coli, and determined the structure at 1.9 Å. The asymmetric unit contains
>>> two protein monomers. Beyond our expectation, strong Fo - Fc density is
>>> present at a cleft of one subunit, but not in the other. Density maps are
>>> given in the snapshots attached to this email. We tried to model Tris or
>>> Bis-tris propane that were used as the purification and crystallization
>>> buffers, but apparently either of them poorly fitted in this density.  The
>>> molecule that can be modeled here seems more likely to be a ligand
>>> comprising 3 or 4 rings with good planarity, however we did not add any
>>> additives in our crystallization trials. So we think it should be something
>>> from E. coli, which has high affinity to our protein. I wonder if anybody
>>> can figure out which molecule well fits to the electron density.
>>>
>>> Best wishes
>>> Wei Liu
>>>
>>>
>>>   
>>> 
>>>
>>
>>
>
> Rohan Bythell-Douglas
> rbyth...@ic.ac.uk
> Section of Structural Biology,
> Dept. Medicine,
> Imperial College
> London SW7 2AZ
>
>
>
>


-- 
Tushar B. Raskar
Project JRF (DBT),
Protein Crystallography Lab,
Department of Biosciences and Bioengineering,
Indian Institute of Technology - Bombay.

Re: [ccp4bb] Density for an unknown ligand

[Bythell-Douglas, Rohan R]

Dear Wei,

I think Prem’s suggestion that the molecule is on a symmetry axis is right. 
There are 2 images in those that you have sent that show a two fold rotation 
axis within the missing density, so I think the density corresponds to two 
molecules. - possibly something like PMSF? Did you happen to use PMSF during 
your purification?

Regards,
Rohan

On 28 Nov 2016, at 11:36, Prem Prakash 
> wrote:

Dear Wei,
I am not sure but is it possible that the crystallization condition you have 
used has already this compound (may be as an impurity) rather than expecting 
this as an extract from E. coli. If that can be searched it may be useful.

Good luck
Have a nice day

On Mon, Nov 28, 2016 at 3:51 PM, LiuWei 
> wrote:
Hi Prem,

Thanks for your response. The compound really looks to be a two-fold symmetry 
related molecule, but I am very sure that it is not located at a symmetry axis. 
It looks like a compound with 3 or 4 terminal ring, could-be two molecules of 
biphenyl enter. Such a compound, however, is almost insoluble, and I wonder if 
it can be copurified with a protein.

Regards
Wei

2016年11月28日 下午02:50，Prem Prakash > 
写道：

Hi Wei,
Is the electron density of this compound lie at the symmetry axis ? It seems to 
me that two planar rings with one connecting oxygen. And the compound is more 
looks like a diphenyl ether to me with its symmetry related molecule.

Hope others will give some more idea about it.

Cheers
P.P

On Sun, Nov 27, 2016 at 4:03 PM, Wei Liu > 
wrote:
Dear all,

We have recently crystallized a recombinant protein produce from E. coli, and 
determined the structure at 1.9 Å. The asymmetric unit contains two protein 
monomers. Beyond our expectation, strong Fo - Fc density is present at a cleft 
of one subunit, but not in the other. Density maps are given in the snapshots 
attached to this email. We tried to model Tris or Bis-tris propane that were 
used as the purification and crystallization buffers, but apparently either of 
them poorly fitted in this density.  The molecule that can be modeled here 
seems more likely to be a ligand comprising 3 or 4 rings with good planarity, 
however we did not add any additives in our crystallization trials. So we think 
it should be something from E. coli, which has high affinity to our protein. I 
wonder if anybody can figure out which molecule well fits to the electron 
density.

Best wishes
Wei Liu


  




Rohan Bythell-Douglas
rbyth...@ic.ac.uk
Section of Structural Biology,
Dept. Medicine,
Imperial College
London SW7 2AZ

[ccp4bb] CCP4 Study Weekend 2017 - EMS back up

[Karen McIntyre]

Dear all

Registration for the CCP4 Study Weekend 2017 is now back online at 
https://eventbooking.stfc.ac.uk/news-events/ccp4-study-weekend-2017-344 .  
There are now approx. 30 places available.

Payment can also be made by credit card through EMS by logging into your 
account at https://eventbooking.stfc.ac.uk/login/ .

Regards

Karen McIntyre
CCP4 Study Weekend Local Organising Committee
Scientific Computing Department - CCP4
R92 1.22 RCaH

Science & Technology Facilities Council
Rutherford Appleton Laboratory
Harwell Campus
Didcot
Oxfordshire
OX11 0FA

Tel +44 (0) 1235 44 5790
Fax  +44 (0) 1235 56 7720

[cid:image003.png@01D2495E.56757F20]@ccp4_mx

**Please note that I only work part-time until 1.30pm**