Dear Jiamu Du,
what were the exact concentrations (Molar values please) of protein and
peptide in the co-crystallization experiment? This may help in
estimating the (possible) occupancy of your peptide.
Jeroen.
JDwrote:
Does anyone know a program can perform the ocupancy refinement?
Or we always only refine B factor to reflect the occupancy?
Thanks
On 4/30/07, *Eleanor Dodson* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
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]>
> <mailto:[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]>
<mailto: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
>
>
> -----Message d'origine-----
> *De :* CCP4 bulletin board [mailto:
CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
> <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> <mailto: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)
--
Jiamu Du
State Key Laboratory of Molecular Biology
Institute of Biochemistry and Cell Biology Shanghai Institutes for
Biological Sciences
Chinese Academy of Sciences (CAS)
--
Jeroen Raymundus Mesters, Ph.D.
Institut fuer Biochemie, Universitaet zu Luebeck
Zentrum fuer Medizinische Struktur und Zellbiologie
Ratzeburger Allee 160, D-23538 Luebeck
Tel: +49-451-5004070, Fax: +49-451-5004068
E-mail: [EMAIL PROTECTED]
Http://www.biochem.uni-luebeck.de
Http://www.iobcr.org
Http://www.opticryst.org
--
If you can look into the seeds of time and say
which grain will grow and which will not - speak then to me (Macbeth)
--
