Re: [ccp4bb] extra high B factor

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CCP4bb <-- 2007 <-- April 2007 <-- 30 April 2007

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Subject: Re: extra high B factor
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2007-04-30

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Subject: Re: extra high B factor
From: "Manfred S {- dot -} Weiss" msweiss {- at -} EMBL-HAMBURG {- dot -} DE
Date: 2007-04-30

Subject: Re: extra high B factor
From: artis {- at -} CHEMISTRY {- dot -} MONTANA {- dot -} EDU artis {- at -} CHEMISTRY {- dot -} MONTANA {- dot -} EDU
Date: 2007-04-30

Shelx can refine occupancies.
Arti
> Does anyone know a program can perform the ocupancy refinement?
> Or we always only refine B factor to reflect the occupancy?
>
> Thanks
>
>
> On 4/30/07, Eleanor Dodson wrote:
>>
>> Well - it is extremely likely that the peptide is partially occupied and
>> the occupancy may well be < 0.5..
>>
>> But at this resolution you are going to have great difficulty deciding
>> whether you should have
>> Occ=1.0
>>
>> Occ = 0.5
>>
>> Occ = 0.33
>>
>> As your Rfactors show it makes very little difference to any scoring
>> system..
>>
>> You can look at difference maps and try to see if one looks flatter than
>> the other ..
>>
>> Even the overall Wilson plot B is not very well determined, so I wouldnt
>> worry too much..
>>
>> Eleanor
>>
>> Jiamu Du wrote:
>> > 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)
>>
>>
>
>
> --
> Jiamu Du
> State Key Laboratory of Molecular Biology
> Institute of Biochemistry and Cell Biology Shanghai Institutes for
> Biological Sciences
> Chinese Academy of Sciences (CAS)
>

Arti S. Pandey
Graduate Student
Chemistry and Biochemistry
Montana State University
Bozeman,MT 59717

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CCP4bb <-- 2007 <-- April 2007 <-- 30 April 2007

Previous message:
Subject: Re: extra high B factor
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2007-04-30 Next message:
Subject: Re: extra high B factor
From: "Manfred S {- dot -} Weiss" msweiss {- at -} EMBL-HAMBURG {- dot -} DE
Date: 2007-04-30