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Novice wants to understand "B-factor"

John Ladasky jladasky at pmgm.Stanford.EDU
Wed Oct 28 06:10:30 EST 1998

Hi there,

	I've been using the program XLOOK version 3.0 to model mutations
in the beta-2 microglobulin protein.  I don't know a whole lot about
crystallography, though.  As I fooled around with the options in XLOOK,
I found an option to analyze the "B factor" of atoms in the crystal
structure.  Apparently, the B factor is a measure of mobility.  Surprise,
I found that one of the residues I was mutating was already quite mobile.
Thus I don't know that I can say much about that residue's behavior.

	What I need to know is exactly how the B-factor is defined.  I
got the impression from talking with my collegues that this was an exper-
imental value, related to the "fuzziness" of the electron density to
which the protein structure had been fit.  A high B-factor indicated
that the atoms were not in a consistent position from unit cell to unit
cell.  If that is the case, XLOOK should not be able to compute B-factors
for the computer-generated mutant molecules, since there is no corres-
ponding crystal struture.  Yet it does.  If someone knows of a good 
reference that I can consult and cite, I would appreciate it.  Thanks!

Rainforest laid low.
"Wake up and smell the ozone,"
Says man with chainsaw.					- John Ladasky

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