 |
 |
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 > [log in to unmask] > > > >