Hi,
If you subtract the average value of refined individual B's of the structure
(you can use baverage for that for example) from the actual refined Biso of
your DNA oligos, and do the same for all the structures you can get an idea of
whether they've become more or less tight upon binding. I assume you used Biso
refinement so the B-column actually reports it. If you used TLS you'll have to
check carefully how you set up refmac to write out the B's so you don't end up
using the residual B's for your calculations.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Michael Murphy
[pn1...@gmail.com]
Sent: Friday, August 24, 2012 9:29 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] is it valid to compare the B factors of corresponding domains
or regions of molecules from different crystal structures
I am looking to compare the B-factors of a particular stretch of DNA bases when
bound by several different proteins. I have crystal structures for each, but
the structures are of different resolutions and also then different Wilson
B-factors. Is it valid to compare those B-factors directly? (probably not) or
to set the B-factors from the different structures to a common scale based on
the Wilson B-factors from their respective data sets?
