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]> 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]>> 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)
-- Jiamu Du State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS)
