Dear Patrick
Long ago we (Cheetham et a (1992) J Molec Biol 224:613-628) did some
refinements on hen lysozyme + substrate complexes at 1.75A and 2A
resolution and showed that B and occupancy are negatively correlated,
especially at 2.0A. In simplistic terms this is because at medium
resolution low density at the atomic position could be the result of
either low occupancy or high B factor. We ran parallel refinements
using assumed occupancies at 0.1 intervals. We looked at R factors but
they werent much help - this was pre-Rfree so the latter might be a
valuable criterion now.
I think a good strategy is to refine your substrate complex at
intervals of o=0.1, 0.2 ... (with a non-complex model at 1-o, ass
positions of side chains and waters may well be different) and look at
the B factors. At the correct(ish) occupancy substrate Bs will be
expected to be similar to those of the ligating residues from the
protein. But it does get to be quite subjective until you have higher
resolution.
best wishes
Pete
On 31 May 2009, at 16:58, Patrick Loll wrote:
Hi all,
I'm looking for a reference to bolster my response to a referee, in
which I defend my decision not to refine the occupancy of a ligand
in structure refined at around 2 A resolution (note the ligand
binding slte lies on a two-fold crystallographic axis, so the
maximum occupancy is 0.5)
I recall reading a paper a LONG time ago (decades) in which someone
described some careful refinement experiments, and concluded that
the correlation between occupancy and B-value is so strong that it
simply makes no sense to "independently" refine both parameters (at
least for light atoms, and in the absence of super high resolution
data).
Alas, all that I recall is this take-home message. I have no idea of
where the paper appeared, or the names of the authors (or indeed, if
I'm even remembering the paper's message correctly). I've tried
trolling through Acta, without success. Does anyone have a better
idea of where I might find this paper, or one espousing a similar
message?
Thanks,
Pat
-------------------------------------------------------------------------------------
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA 19102-1192 USA
(215) 762-7706
pat.l...@drexel.edu
