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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


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Patrick J. Loll, Ph. D.                  
Professor of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
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