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Re: [ccp4bb] extra high B factor |
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CCP4bb navigationCCP4bb <-- 2007 <-- April 2007 <-- 30 April 2007Subject: Re: extra high B factor From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM Date: 2007-04-30 Or we always only refine B factor to reflect the occupancy? Thanks On 4/30/07, Eleanor Dodson > > 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* > > > > > > 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 > > > > *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) CCP4bb navigationCCP4bb <-- 2007 <-- April 2007 <-- 30 April 2007 |
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