I second Phoebe's suggestion. Looks like another molecule to me. If you are doing molecular replacement you may need to get creative about trimming. When we had a case like that it wasn't until the third person worked on it that we go a solution because he trimmed the model differently than the first two who tried.
Kendall On Mar 15, 2013, at 3:29 PM, "Phoebe A. Rice" <pr...@uchicago.edu<mailto:pr...@uchicago.edu>> wrote: What happens if you solvent-flatten/flip/massage that map, but tell the software the solvent content much lower than what you think it is now? Maybe you'll find another copy of the molecule? ________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] on behalf of Andrey Nascimento [andreynascime...@gmail.com<mailto:andreynascime...@gmail.com>] Sent: Friday, March 15, 2013 1:39 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] Strange density in solvent channel and high Rfree 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
