JiamuAccording 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
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-----Message d'origine-----
De : CCP4 bulletin board [mailto: [log in to unmask]]De la part de Jiamu Du
Envoyé : lundi 30 avril 2007 05:57
À : [log in to unmask]
Objet : [ccp4bb] extra high B factorDear 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.
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Jiamu Du
State Key Laboratory of Molecular Biology
Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences
Chinese Academy of Sciences (CAS)