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 <[EMAIL PROTECTED]> 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 [EMAIL PROTECTED] -----Message d'origine----- *De :* CCP4 bulletin board [mailto: [EMAIL PROTECTED] 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)
