[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Temperature factors and Wilson Plots



***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***

Hi,
I have just solved a structure with MAD phasing and am trying to refine
with REFMAC
rather than TNT (which is normally used in this lab).  The model is
fairly consistant with related proteins (so I know there are no gross
errors) and the data are good to 2.4 A.
I ran the data through TRUNCATE, UNIQUE, and then began my refinement
with REFMAC.

The Rfactor (Rfree) dropped from 41% (41%) to 29 % (34%) after 15 cycles

of REFMAC.  They appear to have converged by about cycle 10-12.  The
maps look
good--I can see new side chains where residues were built as alanine,
and continuous
density in the 2 breaks that were not built into the original
experimental map.

As yet, this all seems unremarkable.  What surprised me, however, was
that the
temperature factors for the refined structure were quite high.  They
average temperature
factor is 65 and ranges from 40 to 130.  I browsed through the old posts
to
this list and found a suggestion that your protein atom temperature
factors should
approximate your B from a Wilson plot.  I then looked at my truncate
output
and found the Wilson B value was 56.

I guess I have no real specific questions except to wonder if this is
telling me
something about the quality of either my data, my model, or my crystal.
I have been
unable to find a reference for the acceptable values for a Wilson B
factor.  Would
anyone suspect that I ran TRUNCATE improperly?  Any thoughts would be
appreciated.
Thanks
Andy


--
Andrew M. Gulick                PH   608-262-0529
University of Wisconsin
1710 University Ave.  Madison WI 53705
http://xtal10.enzyme.wisc.edu/~gulick