Quick navigation:        Home   |    Site Map   ||    References   |    Biography   ||    Copyright   |    Other copyright   |    Contact us   |   
Protein structure
 

Re: [ccp4bb] extra high B factor
 

Basic tutorials: 		 
 

CCP4bb navigation

CCP4bb <-- 2007 <-- April 2007 <-- 30 April 2007
Previous message:
Subject: Re: extra high B factor
From: "Manfred S {- dot -} Weiss" msweiss {- at -} EMBL-HAMBURG {- dot -} DE
Date: 2007-04-30 		Next message:
Subject: AW: extra high B factor
From: Herman {- dot -} Schreuder {- at -} SANOFI-AVENTIS {- dot -} COM Herman {- dot -} Schreuder {- at -} SANOFI-AVENTIS {- dot -} COM
Date: 2007-04-30


Subject: Re: extra high B factor
From: mesters mesters {- at -} BIOCHEM {- dot -} UNI-LUEBECK {- dot -} DE
Date: 2007-04-30
Dear Jiamu Du,

what were the exact concentrations (Molar values please) of protein and
peptide in the co-crystallization experiment? This may help in
estimating the (possible) occupancy of your peptide.

Jeroen.



JDwrote:
> 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* < p.dumas@ibmc.u-strasbg.fr
>
> >
> >> 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)


--
Jeroen Raymundus Mesters, Ph.D.
Institut fuer Biochemie, Universitaet zu Luebeck
Zentrum fuer Medizinische Struktur und Zellbiologie
Ratzeburger Allee 160, D-23538 Luebeck
Tel: +49-451-5004070, Fax: +49-451-5004068
E-mail: mesters@biochem.uni-luebeck.de
Http://www.biochem.uni-luebeck.de
Http://www.iobcr.org
Http://www.opticryst.org
--
If you can look into the seeds of time and say
which grain will grow and which will not - speak then to me (Macbeth)
--
ProteinCrystallography.org: Copyright 2006-2007 by Quid United Ltd