Re: [ccp4bb] Off-topic x 2: Chaperone co-expression AND Bac-Mam contract work

[Michał Taube]

Hi,

You can find GroESL expressing plasmid and plasmids with different
chaperones combinations from prof. Bernd Bukau lab on Addgene:

https://www.addgene.org/Bernd_Bukau/

Best
Michal

2017-01-20 3:19 GMT+01:00 Patrick Loll :

> Hello everyone,
>
> Please allow me to kill two off-topic birds with one email ‘stone’:
>
> 1) Can anyone suggest where I can lay hands on the pREP4-GroESL plasmid
> for bacterial co-expression of GroEL and GroES? I’ve checked with the
> original author (Philip Cole), but it’s been decades since he published on
> this, and he’s not sure he can find the plasmid. However, I see recurrent
> (and recent) references to the plasmid in the literature, so I guess that
> it’s loose in the wild…
>
> 2) We’re looking for a contract research organization to do some Bac-Mam
> expression for us (we’re in a hurry to get some results, so we’d like to
> farm it out rather than get the technology going in-house). Can anyone
> recommend a group (ideally in the US, for logistical ease)?
>
> Thanks for any help.
>
> Cheers,
>
> Pat
>
>
>
> 
> ---
>
> Patrick J. Loll, Ph. D.
>
> Professor of Biochemistry & Molecular Biology
>
> Director, Biochemistry Graduate Program
>
> Drexel University College of Medicine
>
> Room 10-102 New College Building
>
> 245 N. 15th St., Mailstop 497
>
> Philadelphia, PA  19102-1192  USA
>
>
> (215) 762-7706
>
> pjl...@gmail.com
>
> pl...@drexelmed.edu
>
>

Re: [ccp4bb] help with Buccaneer

[Carlos CONTRERAS-MARTEL]

You need go first for some density improvement, see

http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=Automated_phase_improvement_with_Parrot

All the best

Carlos


On 01/20/17 05:10, Vikram Dalal wrote:

Hi Everyone,

I want to run the Buccaneer. I need Hendrickson-Lattman 
coefficients for it. How I can find Hendrickson-Lattman coefficients?



*
*

Thanks & Regards,











--
 Carlos CONTRERAS MARTEL, Ph.D.
 (CR1 CNRS)

 carlos.contreras-mar...@ibs.fr

 "Bacterial Pathogenesis Group"
Institut de Biologie Structurale
 UMR5075 CEA-CNRS-UGA

  IBS
  Campus EPN
  71, avenue des Martyrs
  CS 10090
  38044 Grenoble CEDEX 9
  FRANCE


 tel : (+33) (0)4 57 42 86 41

http://www.ibs.fr/groupes/groupe-pathogenie-bacterienne/?lang=fr
http://www.ibs.fr/groups/bacterial-pathogenesis-group/?lang=en

Re: [ccp4bb] help with Buccaneer

[Edward A. Berry]

When faced with a program requiring HL coefficients, and having
phases from a (partial) model, I used to run a ccp4 program called
sigmaa to generate the HL coefficients. I'm not sure if this is
theoretically a good idea, but at least it allows the program to run.

On 01/19/2017 11:10 PM, Vikram Dalal wrote:

Hi Everyone,

I want to run the Buccaneer. I need Hendrickson-Lattman coefficients for it. 
How I can find Hendrickson-Lattman coefficients?


*
*

Thanks & Regards,

[ccp4bb] help with Buccaneer

[Vikram Dalal]

Hi Everyone,

I want to run the Buccaneer. I need Hendrickson-Lattman coefficients for
it. How I can find Hendrickson-Lattman coefficients?




Thanks & Regards,

Re: [ccp4bb] CCP4BB Digest - 18 Jan 2017 to 19 Jan 2017 (#2017-20)

[Jiang Xu]

Hi, everyone,
 I think I found the cause and solution.
 It was due to the project folder of CCP4i,which was set by me to E:/***/**
p reviously, based on which imosflm automatically set its processing folder
also as E:/***/. Because disk E: used to be the flash disk on my computer,
when I unplug the flash disk, the software cannot find the disk then it
will report the error. When I change the project folder in CCP4i to
D:/***/**, which was present on my computer, the problem was solved.
 Best!
Jiang

On Thu, Jan 19, 2017 at 4:00 PM, CCP4BB automatic digest system <
lists...@jiscmail.ac.uk> wrote:

> There are 23 messages totaling 6640 lines in this issue.
>
> Topics of the day:
>
>   1. on space group (2)
>   2. error in startup script
>   3. AW: [ccp4bb] on space group
>   4. *** WARNING SUSPECTED VIRUS, SPAM or SCAM *U* [ccp4bb] error in
> startup
>  script
>   5. Call for MX beamtime proposals at HZB, BESSY II, deadline March 01,
> 2017
>   6. Off-topic, protein in dye-front (ion front?) on native-PAGE (5)
>   7. 6th Edition of the ISBC2017
>   8. Cryosystems series 600
>   9. Unique postdoctoral research opportunity in Tromsø, Norway
>  10. PhD fellowships in Spain
>  11. Anisotropy and temperature (4)
>  12. CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15) (3)
>  13. Joint Postdoctoral Position in the Grishin and Chook Labs at UT
>  Southwestern
>
> --
>
> Date:Thu, 19 Jan 2017 02:33:14 +
> From:Smith Lee 
> Subject: on space group
>
>
> Dear All,
> In the literature, somebody call space group P65 crystal as  "six fold
> screw axis crystal packing", then I would not make any mistake if I call
> P64 space group crystal also as  "six fold screw axis crystal packing",am I
> right?
> I am looking forward to getting a reply from you.
>
> --
>
> Date:Wed, 18 Jan 2017 19:40:30 -0800
> From:Jiang Xu 
> Subject: error in startup script
>
> Hi, Mr/Ms,
>I am a user of CCP4i. I recently discovered that imosflm cannot be used
> on my win7. the error message is shown below.
>[image: Inline image 1]
>   However, when I go to 'bin' folder and double click the imosflm.bat, the
> program can be start up successfully. I don't know what's the problem.
> Thank you!
> Best!
> Jiang Xu
> Department of Molecular and Computational Biology
> University of Southern California
>
> --
>
> Date:Thu, 19 Jan 2017 05:22:24 +
> From:Smith Lee 
> Subject: Re: on space group
>
> Dear All,
> Here may I make my question much clear? For the space group P 65 crystal,
> it seems we can call it "6-fold packing of subunits around a screw axis in
> the crystal". Then for the space group P 64 crystal, can it also be called
> "6-fold packing of subunits around a screw axis in the crystal"?
> Smith
>
> On Thursday, January 19, 2017 11:50 AM, Ethan Merritt <
> merr...@u.washington.edu> wrote:
>
>
>  On Thursday, 19 January 2017 02:33:14 AM you wrote:
> >
> > Dear All,
> > In the literature, somebody call space group P65 crystal as  "six fold
> screw axis crystal packing", then I would not make any mistake if I call
> P64 space group crystal also as  "six fold screw axis crystal packing",am I
> right?
> > I am looking forward to getting a reply from you.
> > Smith
>
> "six-fold screw axis" refers to the symmetry.
>
> "crystal packing" refers to the molecule-to-molecule contacts regardless
> of symmetry.
>
> So no, I don't think "six fold screw axis crystal packing" makes any sense.
>
> --
> Ethan A Merritt, Dept of Biochemistry
> Biomolecular Structure Center,  K-428 Health Sciences Bldg
> MS 357742,  University of Washington, Seattle 98195-7742
>
>
> --
>
> Date:Thu, 19 Jan 2017 08:47:52 +
> From:herman.schreu...@sanofi.com
> Subject: AW: [ccp4bb] on space group
>
> Dear Smith,
>
> I think your question was clear, and the answer you got was clear as well.
>
> However, I think the question you asked was not the right question. You
> want to use a particular phrase to describe your crystal packing and you
> want the CCP4BB to endorse this. When the answer was negative, you asked
> again the same question.
>
> The real question, in my eyes, is “What is the best way to describe my P65
> crystal packing” since I guess you want to use this in your paper. Here I
> would use something like “in the crystal, the subunits are related by a
> 6-fold screw axis”. To be more precise, you could even mention a 65-screw
> axis. Other board members may even have better descriptions.
>
> By the way, 61, 62, 63, 64 and 65 axes are all 6-fold screw axes, but of
> different types.
>
> Best,
> Herman
>
>
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
> Smith Lee
> Gesendet: Donnerstag, 19. Januar 2017 06:22
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] 

Re: [ccp4bb] Off-topic x 2: Chaperone co-expression AND Bac-Mam contract work

[Alexandra Deaconescu]

Hi Patrick:

We have used the Clonetech Chaperone Coexpression Kit. That includes  
GroEL/GroES plasmids.


http://www.clontech.com/BT/Products/Protein_Expression_and_Purification/Bacterial_Expression_Systems/Protein_Folding/Chaperone_Plasmid_Set


Hope this helps,

Alexandra




On 1/19/17 9:19 PM, Patrick Loll wrote:

Hello everyone,

Please allow me to kill two off-topic birds with one email ‘stone’:

1) Can anyone suggest where I can lay hands on the pREP4-GroESL 
plasmid for bacterial co-expression of GroEL and GroES? I’ve checked 
with the original author (Philip Cole), but it’s been decades since he 
published on this, and he’s not sure he can find the plasmid. However, 
I see recurrent (and recent) references to the plasmid in the 
literature, so I guess that it’s loose in the wild…


2) We’re looking for a contract research organization to do some 
Bac-Mam expression for us (we’re in a hurry to get some results, so 
we’d like to farm it out rather than get the technology going 
in-house). Can anyone recommend a group (ideally in the US, for 
logistical ease)?


Thanks for any help.

Cheers,

Pat



---

Patrick J. Loll, Ph. D.

Professor of Biochemistry & Molecular Biology

Director, Biochemistry Graduate Program

Drexel University College of Medicine

Room 10-102 New College Building

245 N. 15th St., Mailstop 497

Philadelphia, PA19102-1192USA


(215) 762-7706

pjl...@gmail.com 

pl...@drexelmed.edu 




--
Alexandra M. Deaconescu, B.E., Ph.D.
Assistant Professor of Molecular Biology, Cell Biology and Biochemistry

[ccp4bb] Off-topic x 2: Chaperone co-expression AND Bac-Mam contract work

[Patrick Loll]

Hello everyone,

Please allow me to kill two off-topic birds with one email ‘stone’:  

1) Can anyone suggest where I can lay hands on the pREP4-GroESL plasmid for 
bacterial co-expression of GroEL and GroES? I’ve checked with the original 
author (Philip Cole), but it’s been decades since he published on this, and 
he’s not sure he can find the plasmid. However, I see recurrent (and recent) 
references to the plasmid in the literature, so I guess that it’s loose in the 
wild…

2) We’re looking for a contract research organization to do some Bac-Mam 
expression for us (we’re in a hurry to get some results, so we’d like to farm 
it out rather than get the technology going in-house). Can anyone recommend a 
group (ideally in the US, for logistical ease)?

Thanks for any help.

Cheers,

Pat



---
Patrick J. Loll, Ph. D.  
Professor of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102-1192  USA

(215) 762-7706
pjl...@gmail.com
pl...@drexelmed.edu

Re: [ccp4bb] CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)

[Phoebe A. Rice]

Excellent point.  I've heard apocryphal stories of someone obtaining beautiful 
salt crystals (magnesium ammonium phosphate) by trying to crystallize an ATPase 
with ADP and Mg++ using (NH4)2SO4 as a precipitant.  Wait long enough, and the 
ADP becomes ATP plus AMP, the ATPase takes the 3rd phosphate off, and then the 
salt crystals grow.  

Yours sounds like a much less depressing "accident"!


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Phil Evans 
[p...@mrc-lmb.cam.ac.uk]
Sent: Thursday, January 19, 2017 4:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)

Remember that 2xADP can disproportionate into ATP + AMP

> On 19 Jan 2017, at 20:54, Panneerselvam, Saravanan 
>  wrote:
>
> Dear All,
> Sorry for the little bit off topic. Is there a possibility for covalent
> bond formation between beta phosphate of ADP and acetate molecule both
> are coordinated by divalent metal ions? I am working on a Kinase
> structure  which was crystallized with ADP and in presence of 1M sodium
> acetate. We observed additional density around ADP that fits perfectly
> like a gamma phosphate , mimicking like ATP bound state, surrounded and
> coordinated by two metal ions(resolution is 1.4A). There is a change in
> space group (from I212121 to P212121 ) and further important
> conformation changes are observed around ATP binding pocket and distant
> region. This is the only xtal we obtained in this space group, and all
> other xtals(measured 10 xtals)  from the same plate belong to I212121.
>
>
>
> Thanks your help and time!
>
> Saravanan
> - Original Message -
> From: "CCP4BB automatic digest system" 
> To: CCP4BB@JISCMAIL.AC.UK
> Sent: Sunday, 15 January, 2017 01:01:37
> Subject: CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)
>
> There are 2 messages totaling 45 lines in this issue.
>
> Topics of the day:
>
>   1. Phenix (2)
>
> --
>
> Date:Sat, 14 Jan 2017 20:58:09 +
> From:D Bonsor 
> Subject: Phenix
>
> Is the phenix website down? Anyone know when it will be back up?
>
> --
>
> Date:Sat, 14 Jan 2017 14:45:06 -0800
> From:Pavel Afonine 
> Subject: Re: Phenix
>
> See notice on Phenix mailing list that answers your question.
>
> On Sat, Jan 14, 2017 at 12:58 PM, D Bonsor 
> wrote:
>
>> Is the phenix website down? Anyone know when it will be back up?
>>
>
> --
>
> End of CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)
> 

Re: [ccp4bb] CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)

[Phil Evans]

Remember that 2xADP can disproportionate into ATP + AMP

> On 19 Jan 2017, at 20:54, Panneerselvam, Saravanan 
>  wrote:
> 
> Dear All,
> Sorry for the little bit off topic. Is there a possibility for covalent 
> bond formation between beta phosphate of ADP and acetate molecule both 
> are coordinated by divalent metal ions? I am working on a Kinase 
> structure  which was crystallized with ADP and in presence of 1M sodium 
> acetate. We observed additional density around ADP that fits perfectly 
> like a gamma phosphate , mimicking like ATP bound state, surrounded and 
> coordinated by two metal ions(resolution is 1.4A). There is a change in 
> space group (from I212121 to P212121 ) and further important 
> conformation changes are observed around ATP binding pocket and distant 
> region. This is the only xtal we obtained in this space group, and all 
> other xtals(measured 10 xtals)  from the same plate belong to I212121.
> 
> 
> 
> Thanks your help and time!
> 
> Saravanan
> - Original Message -
> From: "CCP4BB automatic digest system" 
> To: CCP4BB@JISCMAIL.AC.UK
> Sent: Sunday, 15 January, 2017 01:01:37
> Subject: CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)
> 
> There are 2 messages totaling 45 lines in this issue.
> 
> Topics of the day:
> 
>   1. Phenix (2)
> 
> --
> 
> Date:Sat, 14 Jan 2017 20:58:09 +
> From:D Bonsor 
> Subject: Phenix
> 
> Is the phenix website down? Anyone know when it will be back up?
> 
> --
> 
> Date:Sat, 14 Jan 2017 14:45:06 -0800
> From:Pavel Afonine 
> Subject: Re: Phenix
> 
> See notice on Phenix mailing list that answers your question.
> 
> On Sat, Jan 14, 2017 at 12:58 PM, D Bonsor 
> wrote:
> 
>> Is the phenix website down? Anyone know when it will be back up?
>> 
> 
> --
> 
> End of CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)
> 

Re: [ccp4bb] Anisotropy and temperature

[Stephen Rader]

> Diffraction measurements at a single temperature do not distinguish
> between these two components.  In principle a series of diffraction
> measurements from the same crystal at different temperatures would
> allow partitioning the observed vibrational into the two components.
> [Burgi (2000) Rev. Phys. Chem. 51:275]  So far as I know this has
> been confirmed for small molecule crystals but is too difficult
> experimentally to be worth the trouble for protein crystals
> (and I've tried :-)

In an early effort to investigate the role of protein dynamics in enzyme 
funciton, I studied this question as part of my PhD thesis. We found that, for 
a well-behaved protein that already crystallized well, we were able to nicely 
distinguish thermal disorder (only present at the higher temp, 300 K) from 
static disorder (ie differences protein packing in the crystal or more local 
vibrations that get frozen in). We published it in Rader and Agard, Protein 
Science, 1997 (https://www.ncbi.nlm.nih.gov/pubmed/9232638).

Note that the key for us was to do multiple conformation refinement, so we 
could actually observe the clustering of states in the disordered regions at 
low temp. This required high resolution data to have sufficient refinement 
constraints.

Stephen Rader
Dept of Chemistry
U. of Northern BC

On 2017-01-19, at 1:16 PM, Ethan A Merritt  wrote:

> On Thursday, 19 January, 2017 20:35:14 you wrote:
>> A PhD student asked me what causes diffraction anisotropy.  Quoting from the 
>> Diffraction Anisotropy Server webpage that it is caused by whole-body 
>> anisotropic vibration of unit cells. He asked whether a colder cyrostream 
>> could improve anisotropy. My answer would be yes, as colder temperatures 
>> would lower the vibrations.
>> 
>> My two questions are; (1) am I right? and (2) if so, has it ever been done 
>> before in practice?
> 
> I do not know if there is past work and literature that answers your
> question with specific regard to whole-body anisotropic vibration of
> unit cells.
> 
> However with regard to anisotropy in general you must consider two
> components. 
> 
> (1) Vibration that is still present in the crystal, so that
> atoms or larger groups are moving while the diffraction is measured.
> The vibrational amplitude will be temperature dependent, but
> the anisotropy may remain the same since it depends on the ratio of
> vibration amplitude in different directions rather than the 
> magnitude in any one direction. 
> 
> (2) Vibrational displacement of a group in one unit cell relative
> to copies of the same group in other unit cells that was "locked in"
> when the crystal was frozen.  The frozen crystal captures a 
> sampling of states that were present at room temperature.
> The diffraction experiment sees a positional average over space
> that is equivalent to a single-copy average over time.
> This component is not temperature dependent so long as the 
> crystal stays frozen.
> 
> Diffraction measurements at a single temperature do not distinguish
> between these two components.  In principle a series of diffraction
> measurements from the same crystal at different temperatures would
> allow partitioning the observed vibrational into the two components.
> [Burgi (2000) Rev. Phys. Chem. 51:275]  So far as I know this has
> been confirmed for small molecule crystals but is too difficult
> experimentally to be worth the trouble for protein crystals
> (and I've tried :-)
> 
> This equivalence of states sampled from a single copy over time
> to multiple copies in a frozen crystal is the basis for TLSMD
> analysis.  In the special case of a single molecule per unit cell
> I suppose a one-group TLS treatment reduces to what you originally
> asked about - vibration of whole unit cells - but in general
> it does not.
> 
>   cheers,
> 
>   Ethan
> 
> 
> -- 
> Ethan A Merritt
> Biomolecular Structure Center,  K-428 Health Sciences Bldg
> MS 357742,   University of Washington, Seattle 98195-7742

[ccp4bb] Joint Postdoctoral Position in the Grishin and Chook Labs at UT Southwestern

[Yuh Min Chook]

The Grishin (http://prodata.swmed.edu/ ) and Chook 
(http://www4.utsouthwestern.edu/chooklab/ 
) Labs at UT Southwestern seek a 
recent PhD graduate for a postdoctoral fellow position to study structural 
determinants of nuclear export signals and predict them in protein sequences. 
The project will involve both experimental and computational approaches. The 
experimental aspect requires experience in protein crystallography, biochemical 
and biophysical techniques. The computational aspect will involve sequence 
bioinformatics and structure modeling techniques. Synergy between computation 
and experiment is key to this project.
Applicants should hold a recent PhD degree and have strong laboratory skills in 
all aspects of protein crystallography. Computational biology experience is 
helpful. Good communication and organizational skills are critical.

Please email application to yuhmin.ch...@utsouthwestern.edu 

Application should include curriculum vitae, a summary of current and future 
research interests, a description of past research experience and 
accomplishments, expected availability date and three references.




Yuh Min Chook, Ph.D.
Professor
and Eugene McDermott Scholar in Biomedical Research
Department of Pharmacology &
Department of Biophysics
University of Texas Southwestern Medical Center
6001 Forest Park, ND8.136E
Dallas, TX 75390-9041

(214) 645-6167 (Office)
(214) 645-6168 (Laboratory)
(214) 645-6166 (Fax)
e-mail:  yuhmin.ch...@utsouthwestern.edu
http://www4.utsouthwestern.edu/chooklab/

Re: [ccp4bb] Anisotropy and temperature

[Ethan A Merritt]

On Thursday, 19 January, 2017 20:35:14 you wrote:
> A PhD student asked me what causes diffraction anisotropy.  Quoting from the 
> Diffraction Anisotropy Server webpage that it is caused by whole-body 
> anisotropic vibration of unit cells. He asked whether a colder cyrostream 
> could improve anisotropy. My answer would be yes, as colder temperatures 
> would lower the vibrations.
> 
> My two questions are; (1) am I right? and (2) if so, has it ever been done 
> before in practice?

I do not know if there is past work and literature that answers your
question with specific regard to whole-body anisotropic vibration of
unit cells.

However with regard to anisotropy in general you must consider two
components. 

(1) Vibration that is still present in the crystal, so that
atoms or larger groups are moving while the diffraction is measured.
The vibrational amplitude will be temperature dependent, but
the anisotropy may remain the same since it depends on the ratio of
vibration amplitude in different directions rather than the 
magnitude in any one direction. 

(2) Vibrational displacement of a group in one unit cell relative
to copies of the same group in other unit cells that was "locked in"
when the crystal was frozen.  The frozen crystal captures a 
sampling of states that were present at room temperature.
The diffraction experiment sees a positional average over space
that is equivalent to a single-copy average over time.
This component is not temperature dependent so long as the 
crystal stays frozen.

Diffraction measurements at a single temperature do not distinguish
between these two components.  In principle a series of diffraction
measurements from the same crystal at different temperatures would
allow partitioning the observed vibrational into the two components.
[Burgi (2000) Rev. Phys. Chem. 51:275]  So far as I know this has
been confirmed for small molecule crystals but is too difficult
experimentally to be worth the trouble for protein crystals
(and I've tried :-)

This equivalence of states sampled from a single copy over time
to multiple copies in a frozen crystal is the basis for TLSMD
analysis.  In the special case of a single molecule per unit cell
I suppose a one-group TLS treatment reduces to what you originally
asked about - vibration of whole unit cells - but in general
it does not.

cheers,

Ethan


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] Anisotropy and temperature

[Keller, Jacob]

The actual vibrations don't exist at 100 K (similar to the case of 
B-factors/ADPs, sometimes called mildly misleadingly "temperature factors"), 
but are rather "frozen" where they were when they get cold. So a colder cryo 
stream would not help.

JPK

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of D Bonsor
Sent: Thursday, January 19, 2017 3:35 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Anisotropy and temperature

A PhD student asked me what causes diffraction anisotropy.  Quoting from the 
Diffraction Anisotropy Server webpage that it is caused by whole-body 
anisotropic vibration of unit cells. He asked whether a colder cyrostream could 
improve anisotropy. My answer would be yes, as colder temperatures would lower 
the vibrations.

My two questions are; (1) am I right? and (2) if so, has it ever been done 
before in practice?

Thanks,

Dan

Re: [ccp4bb] CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)

[Phil Jeffrey]

On 1/19/17 3:54 PM, Panneerselvam, Saravanan wrote:

We observed additional density around ADP that fits perfectly
like a gamma phosphate


Hello Saravanan

At 1.4 Angstrom resolution wouldn't that suggest that you've somehow got 
ATP in there ?  I don't think I understand the other option - were you 
proposing a ADP-O-C(O)2 arrangement to explain the density ?  Surely 
that has a rather different shape, considerably different scattering 
power at the center of the terminal group (C vs P) and probably 
different X-O bond lengths.  All of these should show in the density 
maps at 1.4 Å, although the bond length issue could be quite subtle.


Phil Jeffrey
Princeton




mimicking like ATP bound state, surrounded and
coordinated by two metal ions(resolution is 1.4A). There is a change in
space group (from I212121 to P212121 ) and further important
conformation changes are observed around ATP binding pocket and distant
region. This is the only xtal we obtained in this space group, and all
other xtals(measured 10 xtals)  from the same plate belong to I212121.



Thanks your help and time!

Saravanan

Re: [ccp4bb] CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)

[Panneerselvam, Saravanan]

Dear All,
Sorry for the little bit off topic. Is there a possibility for covalent 
bond formation between beta phosphate of ADP and acetate molecule both 
are coordinated by divalent metal ions? I am working on a Kinase 
structure  which was crystallized with ADP and in presence of 1M sodium 
acetate. We observed additional density around ADP that fits perfectly 
like a gamma phosphate , mimicking like ATP bound state, surrounded and 
coordinated by two metal ions(resolution is 1.4A). There is a change in 
space group (from I212121 to P212121 ) and further important 
conformation changes are observed around ATP binding pocket and distant 
region. This is the only xtal we obtained in this space group, and all 
other xtals(measured 10 xtals)  from the same plate belong to I212121.

 

Thanks your help and time!

Saravanan
- Original Message -
From: "CCP4BB automatic digest system" 
To: CCP4BB@JISCMAIL.AC.UK
Sent: Sunday, 15 January, 2017 01:01:37
Subject: CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)

There are 2 messages totaling 45 lines in this issue.

Topics of the day:

   1. Phenix (2)

--

Date:Sat, 14 Jan 2017 20:58:09 +
From:D Bonsor 
Subject: Phenix

Is the phenix website down? Anyone know when it will be back up?

--

Date:Sat, 14 Jan 2017 14:45:06 -0800
From:Pavel Afonine 
Subject: Re: Phenix

See notice on Phenix mailing list that answers your question.

On Sat, Jan 14, 2017 at 12:58 PM, D Bonsor 
wrote:

> Is the phenix website down? Anyone know when it will be back up?
>

--

End of CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)

[ccp4bb] Anisotropy and temperature

[D Bonsor]

A PhD student asked me what causes diffraction anisotropy.  Quoting from the 
Diffraction Anisotropy Server webpage that it is caused by whole-body 
anisotropic vibration of unit cells. He asked whether a colder cyrostream could 
improve anisotropy. My answer would be yes, as colder temperatures would lower 
the vibrations.

My two questions are; (1) am I right? and (2) if so, has it ever been done 
before in practice?

Thanks,

Dan

[ccp4bb] PhD fellowships in Spain

[Mark J van Raaij]

Dear future PhD student,

For prospective PhD students there is the current fellowship call open:
https://obrasociallacaixa.org/el/educacion-becas/becas-de-posgrado/inphinit/programme-description
This is a competitive call with good conditions (salary, mobility, 
complementary training), especially for Spanish standards.
If you go to “Search for a Position” and then look for our centre “Centro 
Nacional de Biotecnologia- CNB”, my vacancy on “Structural Biology on 
Bacteriophage Fibres and Tailspikes" turns up.
If you are interested, please apply. There is no need to contact me, because 
the application process selection committee is independent from the proposed 
supervisors. There are also other structural biology projects, and I think 
selected candidates can choose their favourite project based on the final 
shortlist order.
The deadline for application is 2 February, academic records, reference letters 
and a B2 level certificate in english need to be supplied (nationals of 
english-speaking countries are exempted).

Greetings,

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://wwwuser.cnb.csic.es/~mjvanraaij

[ccp4bb] Unique postdoctoral research opportunity in Tromsø, Norway

[Richard Engh]

Dear all,

I would like to call your attention to a unique postdoctoral fellowship 
opportunity in structural chemistry at the UiT The Arctic University of 
Norway in Tromsø. The project area is "Crystallography, biophysical and 
cheminformatics studies for next-generation kinase inhibitor design".


The program is described in more detail here:

https://euraxess.ec.europa.eu/jobs/163137

The deadline for a preliminary application (2 pages and a CV) is soon, 
February 3.


Promising candidates will then be invited to prepare a more detailed 
application for submission in autumn. If the application is successful, 
the position will be funded starting in 2018.


Besides hosting the Norwegian Center for Structural Biology, Tromsø is a 
fascinating location, with its 2-month long "Polar Night", illuminated 
by some midday twilight and Northern Lights, and its compensating 
2-month long Midnight Sun period. (We don't lack total sunshine hours, 
but have only about 245 sunrises and sunsets per year, depending on the 
view of the horizon from where you live.) As the link above describes 
it, Tromsø is "uniquely located at the top of the world surrounded by 
some of Europe’s last pristine wild nature."


Please feel free to ask me for more details if you are interested.

Sincerely,
Rick Engh

--
Professor Richard Engh
The Norwegian Center for Structural Biology
Forskningsparken 3, Sykehusvegen 23
Fakultet for naturvitenskap og teknologi
Universitetet i Tromsø
9037 Tromsø

[ccp4bb] Cryosystems series 600

[Johan Turkenburg]

We are having a clear out and have several Oxford cryosystems 600 going
spare. They are not in working order, and they are really only for spare
parts. Free to a good home, pick up only.

Contact me off list if you are interested.

If we don't hear within 10 days, they will go in the bin.

Johan

-- 
Dr. Johan P. Turkenburg X-ray facilities manager
York Structural Biology Laboratory
University of York   Phone (+) 44 1904 328251
York YO10 5DD   UK  Fax   (+) 44 1904 328266
http://orcid.org/-0001-6992-6838

Re: [ccp4bb] Off-topic, protein in dye-front (ion front?) on native-PAGE

[zeyaul islam]

Try Tricine gel. It is particularly suited for low molecular wt proteins
and it will give you very good resolution. Even you can run it overnight at
30 V (16-18 hours).

On Thu, Jan 19, 2017 at 9:33 AM, Walt  wrote:

> Hi,
>
> I have a small protein (~9 kDa) with acidic pI (~4).
> When I run 18% native-PAGE, it appears my protein is in the dye front.
> How can I fix this problem? Changing the pH of separating gel
> might help? How about gradient native-PAGE? Thank you!
>
> Walt
>

[ccp4bb] 6th Edition of the ISBC2017

[Jose A. Gavira]

Dear Colleague,
  The Laboratory of Crystallographic Studies is pleased to announce the 6th 
International School on Biological Crystallization (ISBC2017), to be held in 
Granada (Spain) during May 29th to Jun 02nd, 2017. ISBC2017 is intended for 
postgraduate/postdoctoral students and research scientists from industrial and 
academic backgrounds. 
  The International School will provide five days of lectures, posters and 
practical demonstrations focused on the fundamentals of crystallization. The 
aim of the School is to introduce all participants into the fundamental 
knowledge about the behaviour of crystallizing solutions and their applications 
to the field of biological crystallization, including large crystals for 
neutron diffraction and tiny crystals for XFEL. This year we will focus on the 
crystallization of membrane proteins, protein complexes characterization, 
including EM, and biomineralization.
For more information, please visit http://www.isbcgranada.org/.
Best regards,
ISBC 2017 Organizing Committee

LIST OF CONFIRMED SPEAKERS
•   Bernhard Rupp, k. k. Hofkristallamt, US.
•   Terese Bergfors, Uppsala University, Sweden.
•   Janet Newman, CSIRO, Australia.
•   Allan D´Arcy, Actelion Pharmaceuticals, Switzerland.
•   Martin Caffrey, Trinity College Dublin, Ireland.
•   Petra Fromme, Arizona State University, US.
•   Juan Manuel Garcia-Ruiz, IACT, CSIC-UGR, Spain.
•   Jeroen Mesters, University of Lüebeck, Germany.
•   Marc Pusey, iXpressGenes, Huntsville, US.
•   Howard Einspahr, IUCr Journal Comission, US.
•   José A. Gavira, IACT, CSIC-UGR, Spain.
•   Hudel Luecke, University of California, US.
•   Naoko Mizuno, Max Planck Institute, Germany.
•   Sergio Martínez, UGR, Spain.
•   Ivana Kuta Smatanova, University of South Bohemia, Czech Republic.
•   Stephane Veesler, CINam-Marseille, France. (tbc)
•   Claude Sauter, IBMC, CNRS, France.
•   Christian Betzel, University of Hamburg, Germany.
•   Fermin Otálora, IACT, CSIC-UGR, Spain.
•   Guillermo Calero, University of Pittsburg, US.
•   Christian Biertümpfel, Max Planck Institute, Germany.
•   Edward H. Snell, Hauptman-Woodward Institute, Buffalo, US.
•   May Marsh, Swiss Light Source at Paul Scherrer Institut, Swiss.
•   Jose Manuel Martin-Garcia, Arizona State University, US.
•   Giuseppe Falini, University of Bolonia, Italia.
•   Karim Benzerara, Université Pierre et Marie Curie, France.
•   Helmut Cölfen, University of Konstanz, Germany.
•   Monica Budayova-Spano, Université Grenoble Alpes, France.
•   Yves Nys, URA, INRA, France
•   Pavlina Rezachova, University of Prague, Czech Republic.
TOPICS
♣   Nucleation: Classical and non-classical approaches.
♣   Crystal growth kinetics and mechanisms.
♣   Properties of macromolecular solutions (DLS/SAXS).
♣   Screening: The search for crystallization conditions.
♣   Crystallization techniques: Batch, Vapour and Counter Diffusion, How do 
they work?
♣   Crystallization and diffusion transport: gels, microfluidics and 
microgravity.
♣   Crystallization of large crystals for Neutron diffraction.
♣   In vivo crystallization of tiny crystals.
♣   Novel crystallization strategies for XFEL studies.
♣   Serial Crystallography. 
♣   Polymorphism in protein crystals.
♣   Case studies in Membrane Protein Crystallization.
♣   Lipid cubic phase, bicelles and detergents.
♣   Crystallization of Macromolecular Complexes.
♣   Characterization by electron microscopy (EM).
♣   In vitro and in vivo studies of Biomineralization processes.

Re: [ccp4bb] Off-topic, protein in dye-front (ion front?) on native-PAGE

[Artem Evdokimov]

A) change dye or use pure glycerol to load gel

B) change gel pH or add various substances to it (easy to do with the
buffer)

Artem

On Jan 19, 2017 6:34 AM, "Walt"  wrote:

> Hi,
>
> I have a small protein (~9 kDa) with acidic pI (~4).
> When I run 18% native-PAGE, it appears my protein is in the dye front.
> How can I fix this problem? Changing the pH of separating gel
> might help? How about gradient native-PAGE? Thank you!
>
> Walt
>

[ccp4bb] Off-topic, protein in dye-front (ion front?) on native-PAGE

[Walt]

Hi,

I have a small protein (~9 kDa) with acidic pI (~4).
When I run 18% native-PAGE, it appears my protein is in the dye front.
How can I fix this problem? Changing the pH of separating gel
might help? How about gradient native-PAGE? Thank you!

Walt

[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, 2017

[Manfred S. Weiss]

Next MX-proposal application deadline: March 01, 2017 is approaching
http://www.helmholtz-berlin.de/user/beamtime/proposals/index_en.html

Hereby we would like to invite the submission of new proposals for
MX-beamtime at the HZB-MX beamlines for the next beam time period
(08/2017-01/2018).

In order to apply for beamtime, please register at the HZB on-line
access tool "GATE" (https://www.helmholtz-berlin.de/pubbin/hzbgate)
and submit a new beam time application proposal.

What's new: In situ-screening in crystallization plates on BL14.1
will be reinstalled from March 2017 onwards!

HZB provides MX-beamtime at the three MX-beamlines BL14.1, BL14.2
and BL14.3. The three beamlines are equipped with state-of-the-art
instrumentation and are currently the most productive MX-stations
in Germany with over 300 PDB depositions annually. Beamtime is
granted based on the reviewed proposals and on reports from
previous research activities. Please make sure to include them
if available.

Experimental setup:

BL14.1:
- Photon flux: 1.4x10¹¹ Phot/sx100mAx0.05%BW at sample position
  (0.1-1 sec exposure time per frame)
- User defined beam shaping from 50µm-100µm diameter possible
- Pilatus 6M detector, 141mm-680mm max. distance from the sample
- Microdiffractometer (MD2) with Mini-kappa goniometer MK3
- Automatic sample changer (CATS), 90 sample storage capacity
 (SPINE-Pin & EMBL sample magazine compatibility)
- 32-core XEON-CPU server, with 10Gb uplink to Pilatus 6M
- Data collection control via MXCuBE
- EDNA
- Common MX-software installed including XDS, iMOSFLM, CCP4,
  Phenix, SHELXC-E, etc.
- Automated data processing with XDSAPP
- Remotely controlled cryo-shutter for crystal annealing
- Pressure chamber for noble gas derivatization (Xe, Kr
  available upon request)
- AMPTEK-XRF detector and XFEPLOT software available

We are also offering the hard- and software environment for
carrying out:
- UV-RIP experiments at BL14.1. For further information, please visit:

http://www.helmholtz-berlin.de/forschung/funkma/soft-matter/forschung/bessy-mx/ancillary-facilities/uvrip_en.html

BL14.2:
- Photon flux: 1.9x10¹¹ Phot/sx100mAx0.05%BW at sample position
  (0.1-1 sec exposure time per frame)
- Pilatus 3S-2M detector with 1000 micron Si sensor thickness,
  55mm-600mm distance from the sample
- Nanodiffractometer (DESY P11 design) and on-axis sample microscope
- User defined beam shaping from 30µm-150µm diameter possible
- GROB sample changer for SPINE and UNIPUCK support
- 60-core XEON-CPU server, with fibre channel SAN up-link data
  processing environment
- Common MX-software installed including XDS, iMOSFLM, CCP4, Phenix,
  SHELXC-E, etc.
- Automated data processing with XDSAPP
- Amptek XRF detector
- Pressure chamber for noble gas derivatization (Xe, Kr available
  upon request)
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
  8 Mpixel CCD-camera
- UV-Microsprectrophotometer offline setup available
- AMPTEK-XRF detector and XFEPLOT software available

BL14.3:
- Photon flux: 4x10exp10 Phot/sx100mAx0.05%BW at sample position
  (3-20 sec exposure time per frame)
- Rayonix MX-225 X-ray detector, 45mm-380mm distance from the
  sample, 30 deg 2-Theta possible
- MARdtb goniometer
- 60-core XEON-CPU server, with fibre channel SAN up-link data
  processing environment
- EDNA installed and available
- Common MX software installed including XDS, iMOSFLM, CCP4, Phenix,
  SHELXC-E, etc.
- Automated data processing using XDSAPP
- Remotely controlled cryo-shutter for crystal annealing
- HC1c dehydration device installed (please specify HC1-beamtime
  in your proposal if needed)
- Pressure chamber for noble gas derivatization (Xe, Kr available
  upon request)
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
  8 Mpixel CCD-camera

S1-biolab facilities (separate registration required):
- Protein production and purification
- Nanoliter 96 well crystallization plate formulation and storage at
  5 °C and 20 °C
- Biophysical characterization with real time PCR (thermofluor assay)

The HZB-MX group is also providing expert assistance as well as
access to a library of fragments for carrying out crystallographic
fragment-screening experiments. For more information please contact
us at mswe...@helmholtz-berlin.de.

Please visit our web page www.helmholtz-berlin.de/bessy-mx to obtain
updated information about our experimental setup and other
requirements.

Manfred Weiss and the HZB-MX group

--
Dr. Manfred. S. Weiss
Helmholtz-Zentrum Berlin für Materialien und Energie
Macromolecular Crystallography (HZB-MX)
Albert-Einstein-Str. 15
D-12489 Berlin
GERMANY
Fon:   +49-30-806213149
Fax:   +49-30-806214975
Web:   http://www.helmholtz-berlin.de/bessy-mx
Email: mswe...@helmholtz-berlin.de



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Karl 

Re: [ccp4bb] *** WARNING SUSPECTED VIRUS, SPAM or SCAM *U* [ccp4bb] error in startup script

[Harry Powell]

Hi

It looks like you've got the Windows environment variable "MOSDIR" set to "E:\" 
when running CCP4i - I have no idea how that would happen; it's normally set to 
something like C:\MOSDIR. If you haven't got an E:\ drive that would be the 
root of your problem...

Have a look in the list of Windows environment variables - I haven't done this 
since my XP days, but you should be able to find it by looking at the advanced 
system settings, were there should be a button to give you a list of 
environment variables.

Since I'm not familiar with ccp4i on W7 I can't say much more. 

On 19 Jan 2017, at 03:40, Jiang Xu wrote:

> Hi, Mr/Ms,
>I am a user of CCP4i. I recently discovered that imosflm cannot be used on 
> my win7. the error message is shown below.
>
>   However, when I go to 'bin' folder and double click the imosflm.bat, the 
> program can be start up successfully. I don't know what's the problem. 
> Thank you!
> Best!
> Jiang Xu
> Department of Molecular and Computational Biology
> University of Southern California

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

[ccp4bb] AW: [ccp4bb] on space group

[Herman . Schreuder]

Dear Smith,

I think your question was clear, and the answer you got was clear as well.

However, I think the question you asked was not the right question. You want to 
use a particular phrase to describe your crystal packing and you want the 
CCP4BB to endorse this. When the answer was negative, you asked again the same 
question.

The real question, in my eyes, is “What is the best way to describe my P65 
crystal packing” since I guess you want to use this in your paper. Here I would 
use something like “in the crystal, the subunits are related by a 6-fold screw 
axis”. To be more precise, you could even mention a 65-screw axis. Other board 
members may even have better descriptions.

By the way, 61, 62, 63, 64 and 65 axes are all 6-fold screw axes, but of 
different types.

Best,
Herman


Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Smith Lee
Gesendet: Donnerstag, 19. Januar 2017 06:22
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] on space group

Dear All,

Here may I make my question much clear? For the space group P 65 crystal, it 
seems we can call it "6-fold packing of subunits around a screw axis in the 
crystal". Then for the space group P 64 crystal, can it also be called "6-fold 
packing of subunits around a screw axis in the crystal"?

Smith

On Thursday, January 19, 2017 11:50 AM, Ethan Merritt 
> wrote:

On Thursday, 19 January 2017 02:33:14 AM you wrote:

>
> Dear All,
> In the literature, somebody call space group P65 crystal as  "six fold screw 
> axis crystal packing", then I would not make any mistake if I call P64 space 
> group crystal also as  "six fold screw axis crystal packing",am I right?
> I am looking forward to getting a reply from you.
> Smith


"six-fold screw axis" refers to the symmetry.

"crystal packing" refers to the molecule-to-molecule contacts regardless of 
symmetry.

So no, I don't think "six fold screw axis crystal packing" makes any sense.

--
Ethan A Merritt, Dept of Biochemistry
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,  University of Washington, Seattle 98195-7742