There could be a release of sum stress in the crystal with increasing temperature which could even lead to better ordering I can imagine. But that would need a very close inspection and mainly - are the structures completely isomorphous?? I.e. are there changes at all?
If not then I am puzzled. Jan On Thu, Sep 8, 2022 at 3:03 AM Tom Peat <t.p...@unsw.edu.au> wrote: > I think the basic question being asked is why are the B-factors going the > 'wrong' way? > That is, as the temperature increases, one might expect higher B-factors > (at least that is what we are taught) whereas what Matt is seeing is the > opposite- decreasing B-factors as one goes up in temperature (which I also > think is a little strange and I don't have an explanation). > cheers, tom > ------------------------------ > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Phoebe > A. Rice <pr...@uchicago.edu> > *Sent:* Thursday, September 8, 2022 10:48 AM > *To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > *Subject:* Re: [ccp4bb] Lower b-factors with increasing T > > > I guess the big question is what is the question that you’re trying to > address from those numbers? I’d be nervous about making conclusions about > trends in B factors from just 1 data set per temperature. As you probably > know, the B factors will reflect static differences in atomic position > across asymmetric units as well as thermal motion, and it can be difficult > to control variables such as exactly how fast a crystal freezes or how much > trauma it experiences in its journey from sitting happily in a drop to the > frozen state. > > > > *From: *CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Matt > McLeod <mjmcleo...@gmail.com> > *Date: *Wednesday, September 7, 2022 at 1:57 PM > *To: *CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > *Subject: *[ccp4bb] Lower b-factors with increasing T > > Hi everyone, > > I have a series of datasets at 253K (~2.0A), 273K (2.0A), 293K (2.0A), > 313K (2.2A) and I am curious as to the details in determining B-factors. > > I have treated these datasets more-or-less identically for comparison's > sake. I used DIALS to index, integrate, and scale the data. I scaled the > data to a ~0.6 CC1/2 cutoff. > > After fully refining the datasets, there is an odd trend with respect to > temperature (from what has been previously published) and I assume that > this is because of "behind-the-scenes" computation rather than a > biophysical observation. The B-factors slightly decrease from 252-293K, > and then significantly drop at 313K. The maps look pretty well identical > across the datasets. > > 253K - 53.8 A^2 > 273K - 48.4 A^2 > 293K - 45.5 A^2 > 313K - 18.6 A^2 > > I compared the wilson intensity plots from DIALS scaling for 273K and 313K > and they are very comparable. > > I am looking for suggestions as to where to look at how these b-factors > are selected or how to validate that these B-factor are or are not > accurate. Also, any relevant literature would be welcomed. From what I > have read, there is a general trend that as T increase, the atoms have more > thermal energy which raises the b-factors and this trend is universal when > comparing datasets from different temperatures. > > Thank you and happy to supply more information if that is helpful, > Matt > > ######################################################################## > > 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/ > > ------------------------------ > > 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 > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 ######################################################################## 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/
