dear silvia, apart from the resolution, it would be good to know your current refinement strategy and if you fed the structure to pdbredo yet. How did that turn out? the polygon values are picked from structures at similar resolution afaik. In any case, a better list of B-factors is the one you find in the refinement tab "Atomic properties", where phenix lists them for the macromolecules and ligands separately. In that tab you will also find a list of which atoms cause such high ADPs. I think Eleanor is talking about such a screenshot
best, matthias Dr. Matthias Barone AG Kuehne, Rational Drug Design Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany Phone: +49 (0)30 94793-284 ________________________________ From: CCP4 bulletin board <[email protected]> on behalf of Eleanor Dodson <[email protected]> Sent: Monday, January 4, 2021 3:44:33 PM To: [email protected] Subject: Re: [ccp4bb] B-factors very high That polygon is not very useful I dont think. The statistics need to be given separately for structures solved at given resolutions. Eleanor On Mon, 4 Jan 2021 at 14:43, Eleanor Dodson <[email protected]<mailto:[email protected]>> wrote: Well - you dont give the resolution of your data or the "wilson B" which will be recorded in the data processing log. If the resolution is 3A or less a) it is hard to refine a B value, and b) it certainly should be high.. So more information is needed. Eleanor On Mon, 4 Jan 2021 at 14:39, Silvia Napolitano <[email protected]<mailto:[email protected]>> wrote: Dear CCP4 Community, I am currently working on the structure of a monomeric protein of 23KDa. The protein is generally quite "loopy" and I think I am mid-way refinement. At the moment I am struggling, among other things, with an extremely high B-factor and I'm not sure how to lower it. Do you have any suggestions on how I can proceed to obtain a lower average B-factor? (I am sorry if the question is rather naive, but I have worked very little on X-ray structures so far) I attached a screenshot of the polygon obtained from the last refinement (the geometry now should be a bit improved, I am running a new job at the moment). I will be happy to provide further files if needed. Many thanks in advance for your precious help! I wish you a nice start to the new year. Best Silvia ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
