[ccp4bb] Potential weak binding ligand in the active site
Hi all, I apologise in advance for the long post. I am working on solving a structure that looks like it could have a ligand bound in the active site. My data was obtained from a crystal of just the soluble domain of my protein that had been soaked overnight in the ligand solution. The apo crystal structure is already known and so I have solved my structure using phaser MR. I have attached the Aimless report output of my structure at the end of this email. The current R values I have after refinement and adding in all the waters are Rfree: 0.2413 and Rwork: 0.1897. I can clearly see green density that is much larger (only disappears when I contour the Fo-Fc map to about 6 A) than in my control crystal that had been soaked in the same concentration of just solvent (I had used DMF). I am struggling to add in my ligand as it doesn't seem like the entire ligand can fit in the green density. We think it may be because we have only used the soluble domain and so the ligand isn't held very securely since the transmembrane domain is missing. I have been trying to fit in smaller sections of it and doing an occupancy refinement. So far I have been able to get part of the ligand in with an occupancy of about 0.6 but after the refinement run, phenix.refine seems to move this part of the ligand slightly out of the area where I had tried to fit it into the green density. Interestingly, there isn't a big red density in the area that this ligand section has moved to. I would appreciate any advice on how I should proceed with trying to figure out if I have tried the correct section of the ligand and the kind of refinement settings to use with a weak binder. Space Group P212121 Unit cell abc 84.76, 89.84, 91.55 unit cell alpha beta gamma 90, 90, 90 OVERALL LOW RES HIGH RES Low res limit 45.78 45.78 1.94 High res limit 1.9 9.11 1.9 Rmerge 0.234 0.052 1.684 Rmeas 0.244 0.054 1.768 Rpim 0.069 0.016 0.527 Total # observations 663073 6282 36851 Total # unique 55174 579 3359 I/sigma 7.5 27.9 1.4 CC ½ 0.997 0.999 0.747 Completeness % 99 98.7 94.7 Multiplicity 12 10.8 11 *Katherine Lim * *PhD Candidat**e* *School of Biomedical Sciences; School of Molecular Sciences* *Marshall Centre for Infectious Disease Research and Training * *The University of Western Australia* To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Fully funded BBSRC PhD opportunity at the University of Liverpool
Pleas make any suitable candidates aware of this project *https://www.findaphd.com/phds/project/working-at-the-intersection-of-protein-bioinformatics-and-structural-biology-exploiting-protein-structural-ensembles-to-facilitate-structure-solution-from-x-ray-crystallography-and-cryo-em/?p117359* This exciting project involves developing novel tools, using advanced structural bioinformatics methods, to facilitate protein structure determination by X-ray crystallography and cryo-EM. With networking opportunities via the leading software consortia CCP4 and CCPEM, and exposure to experimental methods through time spent in the lab of Owen Davies in Newcastle, this is a chance to work at the cutting edge of applied bioinformatics. thanks Daniel -- Prof Daniel Rigden Institute of Integrative Biology Room 101, Biosciences Building University of Liverpool Crown St., Liverpool, L69 7ZB (+44) 151 795 4467 pcwww.liverpool.ac.uk/~drigden/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Dead link
It looks like someone at CCP4 will have to fix the link to their local copy of the wikidump, but the Phaserwiki link gives you a direct link to all of our documentation. Best wishes, Randy Read > On 18 Dec 2019, at 20:29, David J. Schuller wrote: > > On this CCP4 documentation page: > > http://www.ccp4.ac.uk/html/phaser.html > > The link for "Full documentation" goes nowhere. > > > -- > === > All Things Serve the Beam > === >David J. Schuller >modern man in a post-modern world >MacCHESS, Cornell University >schul...@cornell.edu > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 The Keith Peters Building Fax: + 44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
