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Hi folks:
I am refining an RNA into which Mn++ was soaked. The crystals
diffract well to 2.0 A resolution. I've identified the Mn sites using
anomalous differences and the sites are very clear and make good
chemical sense. I've also added ca. 200 waters using COOT to add
them, to do sanity checks, etc, and have also manually purged
anything that doesn't look sensible. In any case, the following
arises in the absence of the waters as well as their presence:
I have two identical refinements with the following statistics:
Rwork = 15.2 %, Rfree = 22.6 %, rmsd bond = 0.010 A
Rwork = 16.7 %, Rfree = 22.6 %, rmsd bond = 0.005 A
If I do idealized refinement, I can't get the geometry much tighter
than 0.005 A. So it seems any relaxation of the constraints does
nothing for the free R. In addition, The gap between Rwork and Rfree
is significantly larger than in the refinement of the same crystals
in the absence of Mn.
The maps, etc. look sensible. I've done a composite omit map on the
whole structure (in CNS) as a sanity check and the RNA is definitely
correct.
I have to conclude I am doing something stupid. I would be grateful
for any suggestions.
Bill
