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On Sep 14, 2006, at 3:47, Jiamu Du wrote:
Dear All:
I have collected a set of data whose wilson B factor is as high as
70 at 2.8 angstrom.
If you mean that the Wilson B factor for your 2.8 A dataset is about
70, thats quite normal and
well within expected values for that diffraction limit. Still, I
would suggest to check the actual shape
of the wilson plot and make sure it follows expectations ...
I found the R free was so high (R=0.30 Rfree=0.39) during refining
the strucutre, and it is difficult to reduce Rfree.
REM: the goal of refinement is to get a better model, not to reduce
Rfree ;-)
The 2fofc map is well but there are so many random positive peaks
in the fofc map even at 2 sigma counter level.
My question is if the high Rfree is related to the high wilson B
factor.
How can I deal with these high wilson B factor data?
I don't think that the Wilson B has much to do with the high Rfree.
Refinement at 2.8 is difficult.
If that is a mol. replacement solution you refined, you need simply a
lot of manual
work still... it will be tough at 2.8 especially if the model is not
very very similar
(I would consider experimental phasing to be honest)
If its experimental and you are confident you did build a good model,
it might
worth looking at space groups abd/or twinning.
A.
Thanks.
--
Jiamu Du
Key Laboratory of Proteomics
Institute of Biochemistry and Cell Biology Shanghai Institutes for
Biological Sciences
Chinese Academy of Sciences (CAS)
