Dear all, We have solved the problem. Data processing in P1 looks better (six molecules in ASU), and Zanuda shows a P 1 21 1 symmetry (three molecules in ASU), Rfactor/Rfree drops to 0.20978/0.25719 in the first round of refinement (without put waters, ligands, etc.).
Indeed, there were one more molecule in ASU, but the over-merged data in an orthorhombic lattice hid the correct solution. Thank you very much for all your suggestions, they were very important to solve this problem. Cheers, Andrey 2013/3/15 Andrey Nascimento <andreynascime...@gmail.com> > *Dear all,* > > *I have collected a good quality dataset of a protein with 64% of solvent > in P 2 21 21 space group at 1.7A resolution with good statistical > parameters (values for last shell: Rmerge=0.202; I/Isig.=4.4; Complet.=93% > Redun.=2.4, the overall values are better than last shell). The structure > solution with molecular replacement goes well, the map quality at the > protein chain is very good, but in the final of refinement, after addition > of a lot of waters and other solvent molecules, TLS refinement, etc. ... > the Rfree is a quite high yet, considering this resolution (1.77A).(Rfree= > 0.29966 and Rfactor= 0.25534). Moreover, I reprocess the data in a lower > symmetry space group (P21), but I got the same problem, and I tried all > possible space groups for P222, but with other screw axis I can not even > solve the structure.* > > *A strange thing in the structure are the large solvent channels with a > lot of electron density positive peaks!? I usually did not see too many > peaks in the solvent channel like this. This peaks are the only reason for > these high R's in refinement that I can find. But, why are there too many > peaks in the solvent channel???* > > *I put a .pdf file (ccp4bb_maps.pdf) with some more information and map > figures in this link: https://dl.dropbox.com/u/16221126/ccp4bb_maps.pdf* > > * > * > > *Do someone have an explanation or solution for this?* > > * * > > *Cheers,* > > *Andrey* >
