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Re: [ccp4bb] extra high B factor
 

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CCP4bb <-- 2007 <-- April 2007 <-- 30 April 2007
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From: Vineet Gaur vineetgaur1982 {- at -} GMAIL {- dot -} COM
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Subject: Re: extra high B factor
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-04-30


Subject: Re: extra high B factor
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2007-04-30
Dear All:
According to your suggestion, I have set the peptide's occupency to 0.5. Two
strategies were employed.
1. Direct using Refmac restrained refinement for 10 cycles. The B factor
only drops to around 100. R/Rf did not change, either.
2. Direct CNS B-fator refinemen. The B factor drops to a moderate level
60-80, and the R/Rf each increases about 2%.
3. First using CNS B-fator refinemen nad next Refmac restrained refinement.
The B factor drops to 60-80, and the R/Rf did not change.

I think next step TLS refinement should be carried out.


On 4/30/07, Philippe DUMAS wrote:
>
> Jiamu
>
> According to the numbers you have mentioned I conclude that you peptide
> occupancy should be around 60-64 %
> I am interested to know what will be the value that you will obtain after
> refinement...
>
>
> Philippe Dumas
> IBMC-CNRS, UPR9002
> 15, rue René Descartes 67084 Strasbourg cedex
> tel: +33 (0)3 88 41 70 02
> p.dumas@ibmc.u-strasbg.fr
>
>
> -----Message d'origine-----
> *De :* CCP4 bulletin board [mailto: CCP4BB@JISCMAIL.AC.UK]*De la part de*Jiamu Du
> *Envoyé :* lundi 30 avril 2007 05:57
> *À :* CCP4BB@JISCMAIL.AC.UK
> *Objet :* [ccp4bb] extra high B factor
>
> 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)
>
>


--
Jiamu Du
State Key Laboratory of Molecular Biology
Institute of Biochemistry and Cell Biology Shanghai Institutes for
Biological Sciences
Chinese Academy of Sciences (CAS)
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