In a similar vein, there could be effects of variation in humidity. How is humidity controlled at these different temperatures? It can drastically affect crystal ordering, which is of course a key determinant of the eventual Wilson B of a dataset and should be distinguished from a property of the individual atoms when interpreting their refined B-factors.
Gerard. -- On Thu, Sep 08, 2022 at 08:11:08AM +0200, Jan Dohnalek wrote: > 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/ ######################################################################## 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/
