[phenixbb] refinment of ligand

peter hudson peter.hudson.peter at gmail.com
Wed Apr 1 23:53:45 PDT 2009

Hello all

I have refined and built model a dataset of 3.0A resolution dataset. This
model is assocaied with a ligand. After final refinement and model building
i found  a big blob of  Fo-Fc density of around 4sigma level at the
N-terminal of the fianl model. My protein doesnot carry any tag at the
N-terminal. But, the template i have used for the molecular replacement
carrying a tag at the N-termianl, which can occupy only 1/4th of this
positive density after superpostion. My crystallisation conditions component
cannot occupy such higher level of positive density. Since my protein binds
to a ligand, i looked carefully to the positive density and it seems very
similar to the ligand density but its obscure. Refinement after fitting the
ligand leads to very high B-factor of  the ligan, which vary for various
atoms from 50-90 and simultaneously positive density goes off. I also tried
to change the occupancy of the ligand but as i reduce the occupancy the B
factor comes down at the noraml expected average B factor value but again
Fo-Fc density appears in the map over ligand. If i leave to refine the
occupancy to the programme automatically, this lead to the zero occupancy of
the few atoms in the ligand and avearge B factor remains normal.
suggestions  would be appreciated.

Thanks in advance
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