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Napoleao, It is so called alternative origins play a game with you. You do not change your structure by shifting 1/2 translation (or even combination of these translations) into directions of the main axes of your unit cell. Structure factors after this operation stay the same, however phases change systematically, producing however the same map features. Would I be a begin crystallographer now, I would read a bit more old fashioned books on crystallography such as probably Jensen and Stout FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: [log in to unmask] Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 20, 2011, at 07:42 , Napolećo Valadares wrote: > Hello, > I'm observing a very strange phenomena (at least to me, I'm a beginner). It is related to symmetry (I think). > > I got a data set at 1.95A (I/Sigma 3.5, R-Factor and R-meas < 35% in the last shell) and a partially refined solution with R/Rfree 22/24, 166 aminoacids observed and around 30 solvent molecules. I'll call this Solution-1. The refinement was smooth, the densities were very clearly "asking" for the correct missing side chains and the map looks good. > > The space group I'm using is P212121, pointless and XDS agree with that (but me and pointless both have a long history of being wrong about space groups). Phenix.xtriage says there's no twinning. > > I took Solution-1 and used it as a template in a molecular replacement in the same space group (P212121) using the same mtz as the one used to refine the template. I got a different (not superposed in space) solution (called Solution-2, scores by Phaser RFZ=24.2 TFZ=33.0 PAK=0 LLG=1413 LLG=1899) that was readily refined in Phenix to R/Rfree 24/26 without any solvent molecule. > > - The solutions are not superposed in space, although they are near-identical and can be superposed yielding a C-alpha rmd =0.001. > - Both structures present VERY similar density maps. The maps are not superposed in space, but when you "run the chain" in one map in Coot and do the same in the other it they the present exactly the same features. It is impossible to ignore their similarities. > - Both structures and maps present the same origin and unit cell. > - If I add to Solution-2 the equivalent solvent molecules of Solution-1 (I did this by superposing Solution-1 to Solution-2 then copy/pasting the solvent molecules), the R/Rfree become 22/24. This is a clear indication that the solutions are related. > - I can't find any MR solutions using the same template and space groups P222, P2221 and P21212. > > How two different sets of phases can yield maps with the same features? What is happening, wrong space group? I have a feeling my lack of experience is the problem. > Thank you. > Regards, > Napo