Re: [ccp4bb] Coot and XQuartz

Hi Alexandra and Matt I am using OSX Sierra 10.12.2 and Xquartz 2.7.11 and noticing severe degradation in performance with coot and pymol. I can get the program to load up and X11 window comes up. But if I try rotating even a small 30kd protein , the rotation is smooth for two seconds and then the

Re: [ccp4bb] Off-topic question about SEC

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 Univers

[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 thi

Re: [ccp4bb] Off-topic question about SEC

Whoa! Big change! Any possible physiological relevance? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Reza Khayat Sent: Wednesday, January 11, 2017 7:43 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic question about SEC ​All these make sense. Protein is

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

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 "whe

Re: [ccp4bb] Off-topic question about SEC

Yes if it either A) oligomerizes B) significantly changes shape C) aggregates reversibly 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 tha

[ccp4bb] Off-topic question about SEC

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 el

Re: [ccp4bb] PDB validation of structure factors

Hi Claire, I afraid you did not provide enough information to answer your question clearly. What reflection file you submitted to PDB? Note, Phenix refinement outputs MTZ file with four blocks of arrays: - copy of input data (Fobs or Iobs, free-R flags); - data actually used in refinement. Thi

[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

[ccp4bb] Postdoctoral positions available in Melbourne, Australia - protein chemistry and enzymology of DNA repair

Two Postdoctoral Positions are available in the Genome Stability Unit @ St Vincent's Institute in Melbourne, Australia. The Genome Stability Unit studies familial cancer syndromes that cause predisposition to breast/ovarian cancer, leukaemias and other solid tumours. These families inherit a de

[ccp4bb] AW: [ccp4bb] Averaging of different proteins in heteromeric complex

Dear Graham, Best would be to create alternative residues for the two proteins. A could be protein 1, B protein 2. As far as refinement programs are concerned, the alternatives need not to be identical and both alternatives are correctly linked to the common chain. You may have to do some pdb-h

Re: [ccp4bb] Averaging of different proteins in heteromeric complex

Dear Crystallographers, Thank you very much Andrew, David, and Jacob (as well as others outside of the BB) for very helpful input on this problem. It does in fact appear that I have a very nice, statistically disordered structure. In published structures containing statistical disorder authors ha

[ccp4bb] EMBL-EBI is recruiting a Team Leader, Cellular Structure and 3D Bioimaging

Hi all, We are seeking to recruit a Team Leader for the Cellular Structure & 3D Bioimaging team at the European Bioinformatics Institute (EMBL-EBI) located at the Wellcome Trust Genome Campus near Cambridge in the UK. EMBL-EBI is a world-leader in archival and dissemination of 3D biomacromolec

[ccp4bb] EMBO practical course:High-throughput protein production and crystallization

6th-14th of July, 2017 in Harwell (near Diamond/Oxford). Registration deadline 15th of March. http://meetings.embo.org/event/17-protein-production

[ccp4bb] AW: [ccp4bb] To delete main chain or not

Dear Veronica, In this case I would remove the poorly defined residues. They make your model worse. Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von V F Gesendet: Mittwoch, 11. Januar 2017 16:33 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re:

Re: [ccp4bb] To delete main chain or not

Dear Herman and Pavel, > > First a remark: the pdb is a repository and if you insist, they will accept > anything you send them so, yes you can deposit this. > However, your question is off course, do I want to deposit this? One does not > want to end up in the twilight gallery or > deposit a st

[ccp4bb] AW: [ccp4bb] To delete main chain or not

Hi Veronica, First a remark: the pdb is a repository and if you insist, they will accept anything you send them so, yes you can deposit this. However, your question is off course, do I want to deposit this? One does not want to end up in the twilight gallery or deposit a structure where other c

Re: [ccp4bb] To delete main chain or not

Hi, The structure solved with MR; high sequence identity. Disorder occurs > only when ligand is bound. Model is almost 90 % complete except the > disordered region. Please let me know if I can deposit structure as it > is. I took example 1fcc (also low resolution). Seems many residues are > outsi

[ccp4bb] Reminder: Call for access to Synchrotron Beamline Facilities, 2017 - EMBL Hamburg, Germany

*REMINDER: Call for access to Synchrotron Beamline Facilities, 2017 - EMBL Hamburg, Germany* We would like to reminder you about the call for synchrotron beam time applications in biological small-angle X-ray scattering (SAXS) and macromolecular crystallography (MX) for the period April - Dece

Re: [ccp4bb] To delete main chain or not

Hi all, Since some emails were not REPLY ALL, I have answered them here: The structure solved with MR; high sequence identity. Disorder occurs only when ligand is bound. Model is almost 90 % complete except the disordered region. Please let me know if I can deposit structure as it is. I took exam