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: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2009-07-30

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

Dear Vonrhein,

On Fri, Jul 31, 2009 at 12:47 AM, Clemens Vonrhein <
vonrhein@globalphasing.com> wrote:

> Dear Jiamu,
>
> On Fri, Jul 31, 2009 at 12:00:25AM +0800, Jiamu Du wrote:
> > 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?
>
> How do you define 'reasonable'? And why would you want to reduce this
> anyway?
>
> ( 50*76.5 + 20*133.3 ) / 70 = 92.7
>
> which seems fairly close to the Wilson B of 86.3, right?

SO, the B value is right.

> > 2. If it can not be redueced, when I published it, is this value
> acceptable?
>
> Better question: is it the right value? Remember it is
>
> results -> publish
>
> and not
>
> publish <- results
>
> ;-)
>
> If they're correct than they are acceptable (I would accept those
> values).

You can accept these values. But I am not sure that you will be my reviewer
certainly. Someone else can not accept. This is the key point.

>
>
> > 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.
>
> I'm sure hundreds of them ... but I'm sure you want your structure to
> stand on its own, so don't look too close at other structures and
> repeat the various mistakes we've all made and that are now set in
> stone in some old PDB file.

Thanks for your comments and best wishes. This is a great sustainment for
me.

>
>
> Cheers
>
> Clemens
>
> --
>
> ***************************************************************
> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
> *
> * Global Phasing Ltd.
> * Sheraton House, Castle Park
> * Cambridge CB3 0AX, UK
> *--------------------------------------------------------------
> * BUSTER Development Group (http://www.globalphasing.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: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2009-07-30

Next message:
Subject: Re: mosflm and hkl2000
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2009-07-30