It is a clear-cut case of crystal packing disorder. The tell-tale sign is that data can be merged in the higher-symmetry lattice, while the number of molecules in the asymmetric unit (3 in P21) is not divisible by the higher symmetry factor (2, by going from P21 to P21212). >From my experience, this is more likely a case of order-disorder than merohedral twinning. The difference between these two is that structure factors are added for the alternative conformations in the case of order-disorder, while intensities (structure factors squared) are added in the case of merohedral twinning.
Now an important comment on how to proceed in the cases where data can be merged in a higher symmetry, but the structure needs to be solved in a lower symmetry due to a disorder. !Such data needs to be merged in the higher symmetry,assigned R-free flag, and THEN expanded to the lower symmetry. Reprocessing the data in a lower symmetry is an absolutely wrong procedure and it will artificially reduce R-free, as the new R-free flags will not follow data symmetry! Moreover, while this one is likely to be a case of order-disorder, and these are infrequent, reprocessing the data in a lower symmetry seems to be frequently abused, essentially in order to reduce R-free. Generally, when data CAN be merged in a higher symmetry, the only proper procedure in going to a lower-symmetry structure is by expanding these higher-symmetry data to a lower symmetry, and not by rescaling and merging the data in a lower symmetry. Zbyszek Otwinowski > 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 <[email protected]> > >> *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* >> > Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353
