[ccp4bb] Coot and Phenix inappropriately handle heavy atom alternative conformations

[Buth Sergii]

Dear Community,
I work on a crystal structure of a trimeric protein with a total mass of 191 
kDa. Data resolution is 2.4A. Protein crystallizes in the presence of 800 mM 
ZnSO4, and, as a result, contains above 40 zinc ions attached to the protein 
molecule. Certain ions are diffused and/or partially substitutes by water 
molecules; the consistency between diffused/water exchanged NCS related zinc 
residues is limited. Anomalous map does not provide much help for these poorly 
defined sites either.
However, they have to be modeled properly. The best option to model these sites 
is to split them into alternative conformations and place accordingly to 
chemical environment. But as soon as I split a given Zn residue and attempted 
to real space refine its parts in linear mode the Coot prompts “No restrains 
found” error message. Sphere refinement does the job… by putting alt confs 
together, basically overlaying them. For alt confs of often occurring residues 
like Na, Cl, Mg real space refinement works fine in the linear mode, whereas in 
sphere mode it acts as for Zn – overlays alt confs.
Is there a way to make Coot understand and refine alt confs of Zn or any other 
rare occurring residues? Making refinement operational in linear and sphere 
mode would be a great advantage.
Another case is Phenix. ReadySet optimizes geometry and creates restrains only 
for part A of a Zn residue, ignoring part B. Same happens with Phenix.refine. 
Obviously, occupancy refinement for Zn residue parts does not take place.
And the last, but very important. Sphere refinement in Coot becomes very useful 
when treating my Zn sites. However, I wonder where spatial restrains come from? 
Any library like ReadySet uses? mon_lib_list.cif contains restrains only for 
Zn-Cys bond. Restrains, generated by ReadySet cannot be used in Coot.
I run Coot 0.8.8-pre, Phenix 1.11.1-2575 on Ubuntu 16.04 LTS
Here is an example of such a site. 2Fo-Fc@1.2sigma, Fo-Fc@3.5sigma, 
anomap@3.5sigma (yes, anomap is helpful for this site) 
https://dl.dropboxusercontent.com/u/32683446/Disordered_Zn_site.png
Thank you,
Sergii Buth, PhD
Postdoctoral Fellow
University of Texas Medical Branch
Department of Biochemistry and Molecular Biology
301 University Blvd.
5.106 Basic Science Bldg.
Galveston, Texas 77555-0647
P 409-772-6332

[ccp4bb] Completely Off-Topic: Intracellular Glutamate Concentration

[Keller, Jacob]

This is one source paper I found recently, and there are lots of others.


doi:10.1038/nchembio.186

JPK


From: Napoleao Fonseca Valadares [mailto:n...@ifsc.usp.br]
Sent: Thursday, January 12, 2017 12:18 PM
To: Keller, Jacob 
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Completely Off-Topic

Dear Jacob,
You did not miss the 101 class, it is just too much to remember.

E. coli metabolome when growing on glucose (Lehninger, 2013):
http://www.fullonline.org/science/ecoli_metabolome.png

The book does not provide explanation for this, but I remember reading 
somewhere else that glutamate is a metabolic intermediate that mediates osmotic 
regulation. When growing in high osmotic environments,  E. coli accumulates 
glutamate to match the outside osmotic pressure. Hopefully this is not 
incorrect, because that's what I've been telling my students.
Regards,
   Napo


De: "Jacob Keller" >
Para: CCP4BB@JISCMAIL.AC.UK
Enviadas: Quarta-feira, 11 de Janeiro de 2017 22:45:03
Assunto: [ccp4bb] Completely Off-Topic
Dear Crystallographers,

Was anyone else aware that in E coli the intracellular glutamate concentration 
is ~100 mM? Also other cell types (yeast, mammalian) are 10s mM. Anything to 
say about this? I learned of this just recently, and have been amazed about it 
for more than a week. Did I miss this in Biochem 101? Does it matter?

JPK

***
Jacob Pearson Keller, PhD
Research Scientist
HHMI Janelia Research Campus / Looger lab
Phone: (571)209-4000 x3159
Email: kell...@janelia.hhmi.org
***

Re: [ccp4bb] CCP4BB Digest - 10 Jan 2017 to 11 Jan 2017 (#2017-12)

[Whitley, Matthew J]

Hi Claire,

Isn’t the simplest answer just that the EDS server is calculating the 
completeness for a different amount of data (high res limit of 1.92 Å), whereas 
in your Depositor data it was only calculated to a high res limit of 2.1 Å?  
This would probably be the result of you measuring reflections out to 1.92 Å 
during data collection but then manually specifying a 2.1 Å high resolution 
cutoff during refinement.  The refinement program will calculate statistics 
based on your input limit of 2.1 Å, but if the MTZ file actually contains some 
measured data out to 1.92 Å, then the EDS would calculate a different, lower 
completeness if its default setting is simply to use all data present in the 
reflections file.  

Does that explain things, or do you actually have something else in mind as to 
the cause of the discrepancy?

Matthew

---
Matthew J. Whitley, Ph.D.
Research Associate
Angela Gronenborn Lab
Department of Structural Biology
University of Pittsburgh School of Medicine


> Date:Wed, 11 Jan 2017 17:31:38 -0500
> From:Claire Smith 
> Subject: PDB validation of structure factors
> 
> Hello,
> 
> I am trying to run the PDB validation report for a structure that I have
> refined in Phenix (data was analyzed with Xtriage). However, the run
> reports a discrepancy on the completeness of data, as follows:
> 
> % Data completeness  97.4 (29.08-2.10)   Depositor
> 
> (in resolution range)87.5 (29.08-1.92)EDS
> 
> 
> Why this discrepancy?
> 
> 
> Thanks so much,
> 
> Claire

Re: [ccp4bb] Completely Off-Topic

[Napoleao Fonseca Valadares]

Dear Jacob, 
You did not miss the 101 class, it is just too much to remember. 

E. coli metabolome when growing on glucose (Lehninger, 2013): 
http://www.fullonline.org/science/ecoli_metabolome.png 

The book does not provide explanation for this, but I remember reading 
somewhere else that glutamate is a metabolic intermediate that mediates osmotic 
regulation. When growing in high osmotic environments, E. coli accumulates 
glutamate to match the outside osmotic pressure. Hopefully this is not 
incorrect, because that's what I've been telling my students. 
Regards, 
Napo 


- Mensagem original -


De: "Jacob Keller"  
Para: CCP4BB@JISCMAIL.AC.UK 
Enviadas: Quarta-feira, 11 de Janeiro de 2017 22:45:03 
Assunto: [ccp4bb] Completely Off-Topic 



Dear Crystallographers, 

Was anyone else aware that in E coli the intracellular glutamate concentration 
is ~100 mM? Also other cell types (yeast, mammalian) are 10s mM. Anything to 
say about this? I learned of this just recently, and have been amazed about it 
for more than a week. Did I miss this in Biochem 101? Does it matter? 

JPK 

*** 
Jacob Pearson Keller, PhD 
Research Scientist 
HHMI Janelia Research Campus / Looger lab 
Phone: (571)209-4000 x3159 
Email: kell...@janelia.hhmi.org 
*** 

Re: [ccp4bb] Issues with Coot & XQuartz

[hari jayaram]

Hi All

I tried coot and pymol with OSX Sierra 10.12.2 and Xquartz 2.7.11 aall the
way through 2.7.8 after seeing this post.

Pymol ( self compiled 1.8.2 ) 80% of the time on two different machines
stops responding to the mouse.
Coot behaves the same way where smooth rotation my mouse is severely
affected.

Even tried with a new user profile and with no other programs running.

It seems that somethin in Xquartz and OSX Sierra with OpenGL applications
and mouse scrolling is affected.

IOf any Sierra users can confirm or let me know its consistently working (
I see "no issues" randomly 2 out of 10 times) ...let me know

 Thanks a tonne
Hari


On Tue, Nov 22, 2016 at 9:28 AM CROENEN, LAURA E.M. (Student) <
laura.croe...@durham.ac.uk> wrote:

> Hi all,
>
> I downloaded the 2.7.8 package and rebooted which has solved the problem.
> Thank you all so much for your help!
>
> Best wishes,
>
> Laura
> --
> *From:* CCP4 bulletin board  on behalf of Phil
> Evans 
> *Sent:* 22 November 2016 12:45:35
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Issues with Coot & XQuartz
>
> I can run coot locally (though not remotely) on Quartz 2.7.11 (OS X
> Yosemite 10.10.5)
> Phil
>
> > On 22 Nov 2016, at 12:39, Martin Montgomery 
> wrote:
> >
> > Hi,
> >
> > We have had these problems with coot and xquartz versions greater than
> 2.7.8.  This affects coot running locally on OSX and via ssh -XY from the
> mac to our linux workstations.  You should still be able to download the
> xquartz-2.7.8 package (https://www.xquartz.org/releases/XQuartz-2.7.8.html).
> Rebooting after the installation of a later xquartz has not made any
> difference on our macs.
> >
> > Regards
> >
> > MGM
> >
> >
> >
> >
> >> On 22 Nov 2016, at 12:32, Phil Evans  wrote:
> >>
> >> Something we [re]discovered at a recent workshop is that after
> installing Quartz you need to reboot (I believe to start the X11 launch
> daemon). Could this be the problem?
> >>
> >> Phil
> >>
> >>> On 22 Nov 2016, at 11:28, Laura Croenen 
> wrote:
> >>>
> >>> Hello all,
> >>>
> >>> I recently downloaded the CCP4 package on Mac (OS X Yosemite 10.10.2).
> With this I am using the latest update of XQuartz. Some aspects of the
> package (ccp4i2, QtMG) are working fine, but others, inc. Coot, are not
> working at all. When I try to open Coot, it appears to start opening (the
> icon appears at the bottom of my screen) and then disappears, with the
> message:
> >>>
> >>> "student-10-245-174-102:MacOS lauracroenen$ ./coot
> >>> 2016-11-21 17:07:40.946 coot[39004:3369025] script to run
> /Applications/ccp4-7.0/coot.app/../bin/coot
> >>>
> >>> (coot-bin:39010): Gtk-WARNING **: cannot open display:
> >>>
> >>> (coot-crash-catcher.scm:39011): Gtk-WARNING **: cannot open display:"
> >>>
> >>> Has anyone else had this problem? Am I missing something?
> >>>
> >>> Thank you in advance.
> >>>
> >>> Laura Croenen
> >
>

Re: [ccp4bb] Completely Off-Topic

[Harry Powell]

Can I just make the point that the subject "Completely off-topic" is completely 
useless if you're searching through the archives for anything? 

Since it's attracted quite a bit of correspondence, this obviously isn't 
off-topic at all!

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

> On 12 Jan 2017, at 13:24, David Schuller  wrote:
> 
> I wonder if anyone has tried glutamate as a cryprotectant for proteins. If 
> the [] is that high, it may make a stable environment for proteins. I have no 
> idea what effect it might have on ice formation.
> 
> https://amb-express.springeropen.com/articles/10.1186/2191-0855-3-36
> Bacillus subtilis natto: a non-toxic source of poly-γ-glutamic acid that 
> could be used as a cryoprotectant for probiotic bacteria
> 
> 
> 
> Bhat, et al DOI: 10.1186/2191-0855-3-36
> 
> 
> 
> 
> 
>> On 01/11/2017 07:45 PM, Keller, Jacob wrote:
>> Dear Crystallographers,
>>  
>> Was anyone else aware that in E coli the intracellular glutamate 
>> concentration is ~100 mM? Also other cell types (yeast, mammalian) are 10s 
>> mM. Anything to say about this? I learned of this just recently, and have 
>> been amazed about it for more than a week. Did I miss this in Biochem 101? 
>> Does it matter?
>>  
>> JPK
>>  
>> ***
>> Jacob Pearson Keller, PhD
>> Research Scientist
>> HHMI Janelia Research Campus / Looger lab
>> Phone: (571)209-4000 x3159
>> Email: kell...@janelia.hhmi.org
>> ***
>>  
> 
> 
> -- 
> ===
> All Things Serve the Beam
> ===
>David J. Schuller
>modern man in a post-modern world
>MacCHESS, Cornell University
>schul...@cornell.edu

Re: [ccp4bb] Completely Off-Topic

[David Schuller]

I wonder if anyone has tried glutamate as a cryprotectant for proteins. 
If the [] is that high, it may make a stable environment for proteins. I 
have no idea what effect it might have on ice formation.


https://amb-express.springeropen.com/articles/10.1186/2191-0855-3-36


 /Bacillus subtilis/ natto: a non-toxic source of poly-γ-glutamic acid
 that could be used as a cryoprotectant for probiotic bacteria



Bhat, et al *DOI: *10.1186/2191-0855-3-36





On 01/11/2017 07:45 PM, Keller, Jacob wrote:


Dear Crystallographers,

Was anyone else aware that in E coli the intracellular glutamate 
concentration is ~100 mM? Also other cell types (yeast, mammalian) are 
10s mM. Anything to say about this? I learned of this just recently, 
and have been amazed about it for more than a week. Did I miss this in 
Biochem 101? Does it matter?


JPK

***

Jacob Pearson Keller, PhD

Research Scientist

HHMI Janelia Research Campus / Looger lab

Phone: (571)209-4000 x3159

Email: kell...@janelia.hhmi.org 

***




--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

[ccp4bb] CCP4 study weekend 2017 talks

[Charles Ballard]

Dear All

for those of you who could not watch the live stream, Stuart and Laura have got 
the sessions up on 

https://sas.stfc.ac.uk/vportal/index.jsp

Under "CCP4 Study Weekend 2017"

Best wishes

Charles

[ccp4bb] two postdoctoral positions in Oxford

[Lidia Vasilieva]

Two Postdoctoral positions – Towards deciphering mechanisms of transcriptional 
and post-transcriptional gene regulation in eukaryotic cells

Two postdoctoral positions are available early 2017 in the laboratory of Lidia 
Vasiljeva funded by Senior Research Fellowship from the Wellcome Trust at the 
Department of Biochemistry, University of Oxford (http://www.bioch.ox.ac.uk/), 
which is a part of the University of Oxford’s thriving scientific community. 
The laboratory is located in a new  building providing interactive environment 
and various state-of-the-art research facilities.

We are looking for highly motivated candidates with an interest in gene 
regulation in yeast and mammalian cells. The proposed projects will utilize 
state-of-the-art biochemistry and structural approaches combined with the 
functional genome-wide analysis to understand how transcription factors and 
chromatin modifiers regulate transcription of protein-coding and non-coding 
genesis in yeast and mammalian cells. The structural study will be done as a 
part of existing productive collaboration with Jonathan Grimes laboratory at 
STRUBi (Oxford). Candidates trained in protein purification, mammalian cell 
culture, and/or computational biology are encouraged to apply. Applicants 
should have or will shortly obtain a PhD and are expected to be highly 
motivated, with excellent critical thinking skills and will preferably have a 
strong background in molecular biology.
Interested applicant should apply by noon January 12th (today!):


https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_details_form.jobspec?p_id=126656


Let me know if you have any questions.

Dr. Lidia Vasiljeva: 
lidia.vasili...@bioch.ox.ac.uk
Lab web site: http://www.bioch.ox.ac.uk/aspsite/index.asp?pageid=675
phone:(+44)-1865613352

Re: [ccp4bb] Off-topic question about SEC

[Nicolas RICHET]

Dear Reza,
Regarding the molecular weights (60 to 360 kDa), the low salt
concentration seems to drive the assembly of an hexamer.
Salt concentration could have a drastic effect on protein oligomerization.
If your A280 profile of the 360 kDa peak looks good (symmetric and in the
resolution limits), it is very likely to be an "hexamerization"!
As Nicolas FOOS said, you could confirm it using DLS or SEC-MALS (even
better).
Best wishes,
Nicolas




*Nicolas RICHET, Ph. D.Post-Doctoral ResearcherUniversity College Cork*
*School of Microbiology*

*Food Science and Technology Building*

*College Road*

*Cork City*
*IRELAND*


*Mobile: +353 (0)838385151*

2017-01-12 9:26 GMT+00:00 Nicolas FOOS :

> Dear Reza,
>
>
> in the past I had work with protein able to oligomerize reversibly but
> when oligomerization happened, even if I was able to separate and obtain
> monomeric protein,
>
> protein was not in a good condition.
>
>
> Have you try to characterize the two different states by DLS ? To
> discriminate "interaction with resin" that you suspect from oligomerization.
>
> Nicolas
>
>
> Nicolas Foos
> PhD
> Structural Biology Group
> European Synchrotron Radiation Facility (E.S.R.F)
> 71, avenue des Martyrs
> CS 40220
> 38043 GRENOBLE Cedex 9+33 (0)6 76 88 14 87 <+33%206%2076%2088%2014%2087>+33 
> (0)4 76 88 45 19 <+33%204%2076%2088%2045%2019>
>
> On 12/01/2017 01:50, Christopher Colbert wrote:
>
> What's your monomeric molecular weight?  Increased salt concentration can
> easily drive oligomerization.
>
> What is your evidence that it interacts with the resin?
>
> Cheers,
>
> Chris
>
> --
> Christopher L. Colbert, Ph.D.
> Associate Professor
> Department of Chemistry and Biochemistry
> North Dakota State University
> P.O. Box 6050 Dept. 2710
> Fargo, ND 58108-6050
> PH: (701) 231-7946
> FAX: (701) 231-8324
>
> From: CCP4 bulletin board  on behalf of Reza
> Khayat 
> Reply-To: Reza Khayat 
> Date: Wednesday, January 11, 2017 6:42 PM
> To: "CCP4BB@JISCMAIL.AC.UK" 
> Subject: Re: [ccp4bb] Off-topic question about SEC
>
> ​All these make sense. Protein is very strange cause it goes from 60kDa
> (globular) to an apparent 360kDa. Process is reversible too.
>
>
> Reza Khayat, PhD
> Assistant Professor
> City College of New York
> Department of Chemistry
> New York, NY 10031
> --
> *From:* CCP4 bulletin board  on behalf of Keller,
> Jacob 
> *Sent:* Wednesday, January 11, 2017 7:39 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Off-topic question about SEC
>
>
> Yes if it either
>
>
>
> A) oligomerizes
>
> B) significantly changes shape
>
> C) aggregates reversibly
>
>
>
> On option B: Lower NaCl could make the protein “appear” bigger by
> unfolding it a bit; hydrophobic interactions should be weaker in lower NaCl.
>
>
>
> JPK
>
>
>
>
>
>
>
>
>
>
>
> Artem
>
> www.harkerbio.com
>
> "where wild SEC columns roam free"
>
>
>
> On Jan 11, 2017 7:22 PM, "Reza Khayat"  wrote:
>
> Hi,
>
>
>
> Sorry for the off-topic question. Can a protein in lower [NaC] run faster
> on a SEC than at higher [NaCl] (i.e. elute at an earlier volume)? The
> protein elutes well within the resolution limits of the SEC
> with a symmetric gaussian A280 profile. I know that at lower [NaCl] the
> protein can elute later because it may interact with the matrix.  Thanks.
>
>
>
> Best wishes,
> Reza
>
>
>
> Reza Khayat, PhD
>
> Assistant Professor
>
> City College of New York
>
> Department of Chemistry
>
> New York, NY 10031
>
>
>
>
>

Re: [ccp4bb] Completely Off-Topic

[Jon R Sayers]

Following on I read somewhere a while back that potassium conc in E. coli is 
estimated in the 30-300 mM range 
(http://book.bionumbers.org/what-are-the-concentrations-of-different-ions-in-cells/
 
)
 . In other more extremophiles it can be higher  (Extremophiles 
. 2015; 19(2): 
315–325.)Maybe our default buffers should contain K+ and Glu at such high 
conc- though not compatible for IEX of course it would appear that such 
conditions are physiological at least for intracellular bacterial proteins.


Prof. Jon R Sayers FRSB
Dept. of Infection, Immunity & Cardiovascular Disease
University of Sheffield Medical School
Beech Hill Rd
Sheffield S10 2RX
United Kingdom, 

Tel +44 (0)114 215 9552
Fax +44 (0) 114 271 3892
Email  j.r.say...@shef.ac.uk
http://www.sheffield.ac.uk/iicd/profiles/sayers 



> On 12 Jan 2017, at 09:13, Reza Khayat  wrote:
> 
> I don't think this is taught in Biochem101. You didn't miss it. The cytoplasm 
> is quite viscous, like jello. 
> 
> 
> 
> Reza Khayat, PhD
> Assistant Professor
> City College of New York
> Department of Chemistry
> New York, NY 10031
> 
> 
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Tim Gruene 
> [tim.gru...@psi.ch]
> Sent: Thursday, January 12, 2017 3:55 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Completely Off-Topic
> 
> Dear JPK,
> 
> I was not aware of the absolute numbers, but maybe they are little suprising:
> when your tinned food contains 'yeast extract' it is equivalent to monosodium
> glutamate, which is commonly used as flavour enhancing agent.
> 
> I am not a chemist to worry about it, but yeast seems to have a fullfilling
> life with it.
> 
> Best,
> Tim
> 
> On Thursday, January 12, 2017 12:45:03 AM CET Keller, Jacob wrote:
>> Dear Crystallographers,
>> 
>> Was anyone else aware that in E coli the intracellular glutamate
>> concentration is ~100 mM? Also other cell types (yeast, mammalian) are 10s
>> mM. Anything to say about this? I learned of this just recently, and have
>> been amazed about it for more than a week. Did I miss this in Biochem 101?
>> Does it matter?
>> 
>> JPK
>> 
>> ***
>> Jacob Pearson Keller, PhD
>> Research Scientist
>> HHMI Janelia Research Campus / Looger lab
>> Phone: (571)209-4000 x3159
>> Email: kell...@janelia.hhmi.org
>> ***
> 
> --
> --
> Paul Scherrer Institut
> Tim Gruene
> - persoenlich -
> OFLC/102
> CH-5232 Villigen PSI
> phone: +41 (0)56 310 5297
> 
> GPG Key ID = A46BEE1A




Best wishes,


Prof. Jon R Sayers FRSB
Dept. of Infection, Immunity & Cardiovascular Disease
University of Sheffield Medical School
Beech Hill Rd
Sheffield S10 2RX
United Kingdom, 

Tel +44 (0)114 215 9552
Fax +44 (0) 114 271 3892
Email  j.r.say...@shef.ac.uk
http://www.sheffield.ac.uk/iicd/profiles/sayers

Re: [ccp4bb] Off-topic question about SEC

[Nicolas FOOS]

Dear Reza,


in the past I had work with protein able to oligomerize reversibly but 
when oligomerization happened, even if I was able to separate and obtain 
monomeric protein,


protein was not in a good condition.


Have you try to characterize the two different states by DLS ? To 
discriminate "interaction with resin" that you suspect from oligomerization.


Nicolas


Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76 88 14 87
+33 (0)4 76 88 45 19

On 12/01/2017 01:50, Christopher Colbert wrote:
What's your monomeric molecular weight?  Increased salt concentration 
can easily drive oligomerization.


What is your evidence that it interacts with the resin?

Cheers,

Chris

--
Christopher L. Colbert, Ph.D.
Associate Professor
Department of Chemistry and Biochemistry
North Dakota State University
P.O. Box 6050 Dept. 2710
Fargo, ND 58108-6050
PH: (701) 231-7946
FAX: (701) 231-8324

From: CCP4 bulletin board > on behalf of Reza Khayat 
>
Reply-To: Reza Khayat >

Date: Wednesday, January 11, 2017 6:42 PM
To: "CCP4BB@JISCMAIL.AC.UK " 
>

Subject: Re: [ccp4bb] Off-topic question about SEC

​All these make sense. Protein is very strange cause it goes from 
60kDa (globular) to an apparent 360kDa. Process is reversible too.



Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031

*From:* CCP4 bulletin board > on behalf of Keller, Jacob 
>

*Sent:* Wednesday, January 11, 2017 7:39 PM
*To:* CCP4BB@JISCMAIL.AC.UK 
*Subject:* Re: [ccp4bb] Off-topic question about SEC

Yes if it either

A) oligomerizes

B) significantly changes shape

C) aggregates reversibly

On option B: Lower NaCl could make the protein “appear” bigger by 
unfolding it a bit; hydrophobic interactions should be weaker in lower 
NaCl.


JPK

Artem

www.harkerbio.com 

"where wild SEC columns roam free"

On Jan 11, 2017 7:22 PM, "Reza Khayat" > wrote:


Hi,

Sorry for the off-topic question. Can a protein in lower [NaC] run
faster on a SEC than at higher [NaCl] (i.e. elute at an earlier
volume)? The protein elutes well within the resolution limits of
the SEC with a symmetric gaussian A280 profile. I know that at
lower [NaCl] the protein can elute later because it may
interact with the matrix.  Thanks.

Best wishes,
Reza

Reza Khayat, PhD

Assistant Professor

City College of New York

Department of Chemistry

New York, NY 10031

Re: [ccp4bb] Completely Off-Topic

[Reza Khayat]

I don't think this is taught in Biochem101. You didn't miss it. The cytoplasm 
is quite viscous, like jello. 



Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Tim Gruene 
[tim.gru...@psi.ch]
Sent: Thursday, January 12, 2017 3:55 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Completely Off-Topic

Dear JPK,

I was not aware of the absolute numbers, but maybe they are little suprising:
when your tinned food contains 'yeast extract' it is equivalent to monosodium
glutamate, which is commonly used as flavour enhancing agent.

I am not a chemist to worry about it, but yeast seems to have a fullfilling
life with it.

Best,
Tim

On Thursday, January 12, 2017 12:45:03 AM CET Keller, Jacob wrote:
> Dear Crystallographers,
>
> Was anyone else aware that in E coli the intracellular glutamate
> concentration is ~100 mM? Also other cell types (yeast, mammalian) are 10s
> mM. Anything to say about this? I learned of this just recently, and have
> been amazed about it for more than a week. Did I miss this in Biochem 101?
> Does it matter?
>
> JPK
>
> ***
> Jacob Pearson Keller, PhD
> Research Scientist
> HHMI Janelia Research Campus / Looger lab
> Phone: (571)209-4000 x3159
> Email: kell...@janelia.hhmi.org
> ***

--
--
Paul Scherrer Institut
Tim Gruene
- persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A

[ccp4bb] AW: [ccp4bb] PDB validation of structure factors

[Herman . Schreuder]

Dear Claire,

I am not a Phenix expert, but to me the discrepancy lies in the resolution 
ranges reported. The completeness of Depositor goes to 2.1 Å, while the 
completeness of EDS goes to 1.92 Å. Could it be that the cutoff of 2.1 Å was 
used for refinement, while the data were processed to 1.92 Å?

Best,
Herman



Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Claire 
Smith
Gesendet: Mittwoch, 11. Januar 2017 23:32
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] PDB validation of structure factors

Hello,

I am trying to run the PDB validation report for a structure that I have 
refined in Phenix (data was analyzed with Xtriage). However, the run reports a 
discrepancy on the completeness of data, as follows:


% Data completeness  97.4 (29.08-2.10)   Depositor

(in resolution range)87.5 (29.08-1.92)EDS



Why this discrepancy?



Thanks so much,

Claire