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Re: [ccp4bb] Lower completeness, decent R factors, but low B factor... |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: Lower completeness, decent R factors, but low B factor... From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL Date: 2008-08-20 On 20 Aug 2008, at 8:11, Wim Burmeister wrote: > James Pauff a écrit : >> Hello all, >> >> I have a refined structure at 2.6 angstroms that at about 73% >> completeness at this resolution. The I/sigma is about 2.0 at 2.6 >> angstroms, and the omit density for my ligands is great contoured >> at 3.0sigma. My Rcryst is 19 or so and the Rfree is 24.5 or so. >> >> HOWEVER, my mean B value is 13.9, whereas my other 2 structures >> (at 2.2 and 2.3 angstroms, same protein, >95% completeness) have >> mean B values of 22+. Any suggestions as to what is going on >> here? I'm having trouble explaining this. >> >> Thank you, >> Jim >> >> >> >> >> > Dear Jim, > > probably you did not collect your data to the highest possible > resolution. Did you use an inhouse source? You would expect that a > crystal with an average temperature factor of 14 A2 would diffract > to 1.6 A on a synchrotron source. > > Regards > > Wim > Indeed. I could also speculate that if the completeness is 75% because 25% of the *weakest* reflections are missing that would artificially show a lower B factor. Did you look at the actual Wilson B plot - if not do, you can learn a lot of simple things from this graph (its there in the Truncate output, usually part of a scaling run, after SCALA) A. > -- > ********************************************************************** > ********* > Wim Burmeister > Professeur, Membre de l'Institut Universitaire de France > Unit of Virus Host Cell Interactions (UVHCI) UMR5233 UJF-EMBL-CNRS > 6 rue Jules Horowitz > B.P. 181, F-38042 Grenoble Cedex 9 FRANCE > E-mail: wpb@embl.fr > Tel: +33 (0) 476 20 72 82 Fax: +33 (0) 476 20 94 00 > http://www.uvhci.fr > ********************************************************************** > ********* CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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