Sampath Natarajan wrote:
Dear All,
I am refining a structure with 2.5A resolution by refmac5.
I could find the solution by MR using molrep. After fitting the model,
I refined the structure again with 0.3 weighting term, but the output
PDB file shows many splits in the residues. So I used 'auto' as a
weighting term, then I didn't find any splits. At the same time I
noticed that figure of merits is not increasing after model fitting.
But the correlation coefficient is more than 80%. Also while refining
with auto weighting term, the figure of merit goes down about 25% than
previous.
Finally I find that some of the residues show high B factor.
Could anyone give suggestions to reduce the B-factor?
Thanks in advance!
Yours sincerely,
Sampath
For 2.5A data, the refmac default X-ray weighting factor of 0.3 is
typically much too high, and does not appropriately apply geometric
constraints. (That is why your proteins chains are breaking up.) An
alternative to the auto weighting function is to set your own weighting
factor and monitor rmsBOND and rmsANGLE deviations in the final model.
If the final rmsBOND is on the order of 0.015 A and rmsBOND is on the
order of 1.5 degrees then your choice of weighting factor is reasonable.
For medium resolution data in the 2.2-2.8A range, I would start with an
X-ray weighting factor of about 0.05 or so.
Cheers,
--
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