Re: [ccp4bb] question of extra high B factor

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

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Subject: Re: question of extra high B factor
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2009-07-30

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From: Huiying Li hli {- at -} CRYSTAL {- dot -} BIO {- dot -} UCI {- dot -} EDU
Date: 2009-07-30

Subject: Re: question of extra high B factor
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2009-07-30

I am using TLS refinement with Phenix for the structure refinement.

On Fri, Jul 31, 2009 at 12:00 AM, Jiamu Du wrote:

> Dear All,
> I am refining a structure of a complex between of 50kD protein and a 20kD
> glycosylated protien. The data is of 2.9 A resolution. The wilson B factor
> is as high as 86.3 A^2.
> The refinement seems well with R/Rf of 0.21/0.25. But the B-factor is extra
> high. For the 50kD part, the average B factor is 76.5 A^2. But the B factor
> of the 20 kD glycosylated protein is as high as 133.3 A^2. Although the
> electron density looks fine, even the sugar chain is seen clearly.
> My question is:
> 1. How to reduce the B factor to a reasonable level?
> 2. If it can not be redueced, when I published it, is this value
> acceptable?
> 3. In the same of similar resolutionIs, is there some other structures like
> this situation? A component or a subunit of the protein has a extra high B
> factor as high as 130.
>
> Thanks and best wishes.
>
>
> --
> Jiamu Du, Ph.D.
> State Key Laboratory of Molecular Biology
> Institute of Biochemistry and Cell Biology
> Shanghai Institutes for Biological Sciences
> Chinese Academy of Sciences
> 320 Yue-Yang Road
> Shanghai 200031
> P. R. China
> Tel: +86-21-5492-1117
> E-mail: jiamudu@gmail.com
>

--
Jiamu Du, Ph.D.
State Key Laboratory of Molecular Biology
Institute of Biochemistry and Cell Biology
Shanghai Institutes for Biological Sciences
Chinese Academy of Sciences
320 Yue-Yang Road
Shanghai 200031
P. R. China
Tel: +86-21-5492-1117
E-mail: jiamudu@gmail.com

CCP4bb navigation

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

Previous message:
Subject: Re: question of extra high B factor
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2009-07-30

Next message:
Subject: Coot:findwaters in REFMAC
From: Huiying Li hli {- at -} CRYSTAL {- dot -} BIO {- dot -} UCI {- dot -} EDU
Date: 2009-07-30