On Wednesday, 02 August, 2017 21:58:07 Asmita Gupta wrote:
> Hi,
>
> Thanks for the response!
>
> What I have are crystal structures of the same protein in multiple
> conformations, solved by different groups. I wanted to calculate the
> residue-wise B-factors for each of these structures and compare how the
> values are changing for corresponding residues in these different structures.
> e.g. B-factor variation in residue number 200 (Ala) in 10 different
> conformations of a protein.
>
> Hope I have been able to answer the question!
But what is the biological question?
You haven't learned much if all you can say is
"The B factor of residue 200 is higher in this structure".
Do you not have a larger question in mind - on the order
of "ligand binding a site X correlates with reduced
mobility of loop A-B"?
For such questions I suggest (as I always do :-) using TLSMD
analysis rather than examining individual B factors.
That allows you to say something like "in structure #1 we
can identify a distinct group motion of residues in loop A-B,
whereas in structure #2 loop A-B appears to move in concert
with the entire subdomain XX". This is not the same thing
as saying individual B factors are higher or lower.
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
