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 <B = 130>
Occ = 0.5 <B = 100>
Occ = 0.33 <B = ??? 80???>
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* <[EMAIL PROTECTED]
<mailto:[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] <mailto:[EMAIL PROTECTED]>
-----Message d'origine-----
*De :* CCP4 bulletin board [mailto: CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>]*De la part de* Jiamu Du
*Envoyé :* lundi 30 avril 2007 05:57
*À :* CCP4BB@JISCMAIL.AC.UK <mailto: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)
