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: [log in to unmask]
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
From: CCP4 bulletin board [[log in to unmask]] on behalf of Michael Murphy [[log in to unmask]]
Sent: Friday, August 24, 2012 9:29 PM
To: [log in to unmask]
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?
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