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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: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK Date: 2008-08-22 Rerun truncate on your data ans look at the graphs - they often give clues if the distribution is distorted.. Eleanor PS - maybe we are a nervous lot, but we always re=process synchroton data again at home with time to think about it.. James Pauff wrote: > Hello all, thank you for the responses. Just to clear up a couple of things... > 1) My dataset was acquired on a synchrotron and scaled/truncated there. To my knowledge they used the same procedure as for other structures that we have obtained there...which have had no B factor issues. Granted, our modified protein is of a different spacegroup than previous. > > 2) I have not used/touched the TLS parameters at all. > > The idea that our 73% completeness (thus lacking 27% of the 'weakest' reflections) has lead to an artificially low B factor sounds most appealing at this point? > > As usual, I greatly appreciate all of your insights here! > > Best, > Jim > > > --- On Wed, 8/20/08, Eleanor Dodson > > >> From: Eleanor Dodson >> Subject: Re: [ccp4bb] Lower completeness, decent R factors, but low B factor... >> To: pauffjm@yahoo.com >> Cc: CCP4BB@jiscmail.ac.uk >> Date: Wednesday, August 20, 2008, 4:30 AM >> James Pauff wrote: >> >>> 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 >>> >>> >>> >>> >>> >>> >>> >> Have you used TLS - listed B factors will then be given >> relative to the >> TLS parameters. You need to run tLSANL to get a more >> realistic value. >> Eleanor >> >> >> But in fact temperature factors are rather harder to >> estimate at lower >> resolutions than higher. Look at your >> >> ( part of a REFMAC loggraph) and you can see that sometimes >> the overall >> scaling struggles to get a reasonable fit.. >> > > > > > > CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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