Dear Xinghua, the solvent content provided by yhe Matthews-program is certainly correct. Whether or not it applies to you protein is a different issue. With only 2 molecules in the asymmetric unit the solvent content rises to 65%, and this is stll perfectly fine for proteins. So carry out molecular replacement with only two molecules and start model building and refinement.
Your previous message sounds as though to started refinement directly after molecular replacement. I would strongly discourage you from this practice (which somehow seems to be stuck in the heads of many people). After molecular replacement you should check the result with the model building program of your choice and correct as many errors as possible before running a refinement program. Tim On Fri, Jun 25, 2010 at 01:54:05PM +0800, xinghua qin wrote: > Hi everyone: > Thanks for all the responses. > The Matthaws-cell content analysis programe in CCP4 package gives the > results: 47% solvent content and 3 molecules in asu with 87% confidence. > the space group is P3121. how to carry out self rotation function? can > phaser do that work? If there areTwo moleculars in asu ,no clashes and the > TF values are above 10.but if three, the clashes are too much and TF valur > is about five. > And how to calculate the solvent content? Is the calculated solvent content > with the Matthews-cell content analysis programe not always right? > Best regards > > Xinghua Qin > On Fri, Jun 25, 2010 at 10:42 AM, Vineet Gaur <vineetgaur1...@gmail.com>wrote: > > > Hi > > It would b good if u can mention the solvent content and space group along > > with the no. of molecules in asu/ > > > > u can carry out self rotation function to check the no of mol in asu > > best > > vineet > > On Fri, Jun 25, 2010 at 6:42 AM, xinghua qin <xtal...@gmail.com> wrote: > > > >> hi CCPeers > >> The Matthews coefficient of my protein is 3 calculated with > >> matthews-cell content analysis CCP4 programe with 87% confidence , but > >> when > >> doing the refinement the third molecular couldn't get into the unit cell > >> because of too many clashes.Deletion of the clashed AA did not work well, > >> Then I used two molecules in the unit cell, After refining with Refmac, I > >> found that the R factor is 0.29, R free is 0.40.I believe the value can be > >> better with the real space refinement.But the question is that can the > >> calculated Matthews coefficient be wrong? > >> > >> Best regards > >> > >> Xinghua Qin > >> > >> -- > >> Xinghua Qin > >> College of Biological Sciences > >> No.2, Yuan Ming Yuan West Road > >> Haidian District，Beijing，China，100094 > >> Tel: +86-10-62732672 > >> > > > > > > > -- > Xinghua Qin > College of Biological Sciences > No.2, Yuan Ming Yuan West Road > Haidian District，Beijing，China，100094 > Tel: +86-10-62732672 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
signature.asc
Description: Digital signature
