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On Wed, 17 May 2006, fang sheng wrote: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > Hello, All, > > I have a 3.0 A data set in space group I41 and got a solution from MolRep. > When I put it for refinement in refmac under " restrained refinment " > patten, I get 28.7% and 35.5% for R and Rfree, respectively. The B-factor is > only 18.78, unusally low compared to 45.0 ,which is for 2.3 A data from its > mutant. I assume a similar B factor between them since there is one amino > acid residue difference out of 500 residues in total. Am I wrong about it? > The worse is refinement only gets Rfactor drop a little and Rfree increase > the same amount.B factor keeps getting lower and lower. fixing B-factor > within the range of 20 -200 doesn't do much good. > > The Rmerge in highest resolution shell is kind of high, as 60% while other > factors seem all decent. I though it was fine. But now the low B factor and > high Rfree make me think maybe I should have data reprocessed for a lower > Rmerge. I played with weighting term( 0.05-0.20) and doesn't change things > much.Does anyone have the same experience and please comment on it. Any > imput is appreciated. > > Regards > > Fang Sheng > Are you wrong about it? Yes, I think so: overall temperature factor (either for the data, from a Wilson plot, or average individual isotropic temperature factor) is strongly dependent on: crystal quality itself (inherent to the one crystal the data was collected from); crystal handling or mis-handling. Usually, the maps from data with low B factor (or from a model with low values of refined B-individual) should be nicer looking than if the B value is high. I only replied to one part of your message. Fred. -- s-mail: F.M.D. Vellieux (B.Sc., Ph.D.) Institut de Biologie Structurale J.-P. Ebel CEA CNRS UJF 41 rue Jules Horowitz 38027 Grenoble Cedex 01 France Tel: (+33) (0) 438789605 Fax: (+33) (0) 438785494 e-mail: [EMAIL PROTECTED]
