Dear Zbyszek, I am concerned that the unmerged data would be bypassed and not preserved in your recommendation. I also find it counter intuitive that the merged data would then be unmerged into a lower symmetry and be better than the unmerged data; there is I imagine some useful reference or two you can direct me to that may well correct my lack of understanding. Thirdly I think this a very likely useful case to preserve the raw diffraction images. All best wishes, John
Prof John R Helliwell DSc On 19 Mar 2013, at 14:37, Zbyszek Otwinowski <zbys...@work.swmed.edu> wrote: > 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 <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* >>> >> > > > Zbyszek Otwinowski > UT Southwestern Medical Center at Dallas > 5323 Harry Hines Blvd. > Dallas, TX 75390-8816 > Tel. 214-645-6385 > Fax. 214-645-6353
