Shelx can refine occupancies. Arti > 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) >
Arti S. Pandey Graduate Student Chemistry and Biochemistry Montana State University Bozeman,MT 59717
