Re: [ccp4bb] extra high B factor

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: problem with HKL2000 license
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2007-04-30

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Subject: Re: problem with HKL2000 license
From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2007-04-30

Subject: Re: extra high B factor
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-04-30

Hi Jiamu,

is the high B-value of your protein due to motions, which are not
modeled appropiately ? Which program by the way are you using for
refinement ? Then the TLSMD server might help you here. Monomer or
multimer in the asu ? NCS used, if so checked that they actually follow
NCS and you're not forcing them ?

How does your difference density map look like around your ligand ?

Jürgen

Jiamu Du wrote:

> Dear All:
> I am refining a protein-peptide complex struture at 2.6 angstrom
> resolution.
> The data was obtain from a co-crystal and the wilson B factor of the
> data is about 70.
> The affinity between protein and peptide is about 10E-7 to 10E-8 molar.
> Protein fragment of the structure has a common B facor about 50.
> But surprisingly, the average B factor of the peptide is as high as
> 130, although the peptide can be clearly traced from the the electron
> density map. All residues of the peptide have such a high B factor.
> My question is how can I reduce the abnormal high B factor to a common
> level or if this high B factor acceptable.
> And another question is if this high B fator will influence the final
> refiment level.
>
> Thanks.
>
> --
> Jiamu Du
> State Key Laboratory of Molecular Biology
> Institute of Biochemistry and Cell Biology Shanghai Institutes for
> Biological Sciences
> Chinese Academy of Sciences (CAS)

--
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: problem with HKL2000 license
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2007-04-30

Next message:
Subject: Re: problem with HKL2000 license
From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2007-04-30