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occupancy refinement

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We are trying to refine enzyme-bound metal ions and other ligands against
data of 1.5-1.6 A resolution.  Will there be a strong correlation between
occupancy and temperature factor refinements be at this resolution?  While
we have nice SIGMAA weighted maps from REFMAC showing the ligands, the
temperature factors refine to higher values than the residues they bind to.
In one instance we have a Ca++ with a refined B-factor of about 15A**2 bound
to protein carboxyl oxygen atoms in the 4-10A**2 range.  How accurately can
one distinguish the Ca++ (18 e-) from a partially occupied Ca++ or from Mg++
(10 e-) by refining temperature factors and/or occupancies at this
resolution?  Finally, what is the consensus about refining water occupancies
at this resolution?  Cheers!

Dave Timm
Indiana Univ. School of Medicine
Dept of Biochemistry
Medical Sciences Building
635 Barnhill Drive
Indianapolis, IN 46202