The other approach is to choose a reasonable B-factor from the atoms and ligands in the vicinity, fix the B's, and then refine the occupancy.
It is true that the occupancy and B-factor of an atom are highly correlated with full-matrix least-squares refinement. The only discrimination comes from high-resolution data since the shape of the B-factor and occupancy are different, i.e., the functional descriptions and refinement variables are not the same, so there can be some discrimination. This is difficult even with high-resolution small molecule structures. Bernie Santarsiero On Sun, May 31, 2009 11:12 am, Poul Nissen wrote: > 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 >> >> >> >> > >
