On Friday 22 May 2009 11:10:16 Francis E Reyes wrote:
> Hi all,
>
> Maybe this is more of a statistics/normalization question, but say you
> have the same molecule crystallized in two different states. How would
> you put their refined b-factors (directly from the pdb) on the same
> scale and say compare the b-factors of residues in the binding pocket?
> I figure some normalization scheme is involved, but are there any
> specific examples ? (quantile normalization? z-score?)
>
> Are there any papers that discuss interpretation of b-factors (being a
> crystallographic property) to the relative dynamics/flexibility of the
> residue in the crystal (and subsequently in solution if the residue is
> not a crystal contact?). I'm particularly interested in the dangers of
> such an interpretation.
[insert standard plug for TLSMD analysis]
I think that comparing individual B factors is the wrong way to go.
There is much more statistical power in looking at the joint distribution
of B values in 3-space. That is the basis for the analysis performed by
the TLSMD server
http://skuld.bmsc.washington.edu/~tlsmd
We have demonstrated that this kind of analysis can pick out similar
features (hinges, domain boundaries, flexible groups, vibrational modes)
not only in multiple crystal forms of the same protein but also across
structures of homologous proteins.
The TLSMD web site contains more discussion and links to publications.
Ethan
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
