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
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
Dear Pat,
You don't say how large your ligand is, but if the occupancy is
refined as a single parameter so that all the atoms in the ligand
are constrained to have the same occupancy, it should be rather
well-defined and not highly correlated with the B-values. By
the way, I was not your referee!
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 hi
Sorry Charlie for the late reply.
I'm using the CFX96 5 channel with Sypro and other dyes. I tested the
machine against the Eppendorf product nd decided to go for the Biorad
version as running identical samples gave better results on the
Biorad. This could be a machine specific problem but o
Simple test is to vary the occupancy (say increments of 0.1) and check for
residual densities following quickie refinements on each. Then at least you
know if you can make a conclusion or not.
I suppose you could also try refining coupled occupancies on ligand-sized
chunks of the protein to g
