Hello:
this may not be 100% relevant to the discussed issue but to add a data
analysis perspective: to be able to compare B factors in different
structures, they need to be scaled. We used primitive but in my opinion
functional linear scaling from 1 to 100 (Schneider et al. Acta Cryst D,
D70: 2413 (2014)).
We observed clear correlation between B factor distributions and
resolution. At "high resolution" (<1.9 Å) Bs correlate with the expected
physical behavior of atoms (Bs of the AAs in hydrophobic core << solvent
exposed AAs < solvent at the interfaces < solvent at the surface). In
"low resolution" structures, 2.5-3.0 Å, all atoms have indistinguishable
behavior.
We analyzed only structures determined at cryo conditions.
Bohdan, bs.structbio.org
On 2022-09-08 09:17, Gerard Bricogne wrote:
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/
########################################################################
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/
