If there is serious doubt of a full occupancy of the ligand and it is
of importance for the interpreation it can in fact be handled and even
at lower resolution (we have done it 2.8 Å resolution for PDB 2C8K for
example) - I'm not the referee but maybe he/she is right ;-)
You need not refine q and B at the same time, but rather just
"titrate" q - i.e. refine the structure with fixed q changed in steps
of 0.1 and perhaps later 0.05 - the q that produces the most
reasonable B-factor distribution (with ligand B comparable to
surrounding regions) and the most clean difference map can be used.
Poul
On 31/05/2009, at 17.58, 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
