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 <[log in to unmask] > 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
[log in to unmask]
 

-----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 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)