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Dear Chen, You have to be careful in interpreting your "the pseudo-procession images.” If the intensities of the reflections are not well recorded (due to misalignment), you can’t draw any real conclusions. Given your trigonal plane (hk0, i.e, your left-hand image), it does not show 3-fold symmetry, but quasi-symmetry. What I see is a lot of breaks in the presumed 3-fold symmetry. You can see that when you walk out from the origin, then look at any line and any presumed symmetric line (just write down the intensities as absent, weak, medium, strong), and you will see what I mean. But if the "the pseudo-procession image” is not perfect, all bets are off. (Having done data collection on the old Supper and Enraf-Nonius cameras, many older crystallographers got pretty comfortable doing this.) >> I just don't have much experience, but assuming it is P1, >> is it possible for NCS to have such perfect absences? Yes, but to a point! I say this because of a case I ran across as a graduate student. Using real procession images, I was sure that the space group was orthorhombic, but it turned out to be monoclinic at higher resolutions (4.5 A and beyond). As my protein had 222 symmetry and was near a special position, the crystal’s diffraction showed pseudosymmetry at lower resolution (~5A) that was broken at higher resolution. Could your protein have 3-fold or 32 molecular symmetry? At low resolution it could be reflected in the diffraction pattern if properly oriented. My advice for now is to stay in P1 and determine where the molecules you see are located in the unit cell. Also, what does a self rotation function tell you? Best of luck, Michael **************************************************************** R. Michael Garavito, Ph.D. Professor of Biochemistry & Molecular Biology 603 Wilson Rd., Rm. 513 Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334 Email: [log in to unmask] **************************************************************** > On Jul 19, 2016, at 3:22 PM, Chen Zhao <[log in to unmask]> wrote: > > Dear crystallographers, > > I am now working on a 3.6 A dataset and I have some doubts on space group determination. Most importantly, I would like to learn and understand more about this procedure. > > The data quality is not ideal and there is some radiation damage. Base on CORRECT in XDS, it looks like P3_12, P3_1, C2 and P1 are all compatible with the reflection intensities. I attached the screenshot of the table here. > > MR is able to find a single solution (partial model occupies 63% of the whole) with high score in all space groups listed above. However, after a refmac run, only space group P1 gives a R-free below 40%, and all other space groups yields R-free factors about 50%. (I think I used the Rfree generated based on point group symmetry but I might not have done it in the right way.) Besides, the desired electron density (although only a very small region is clear) is the best in P1, present in P3_1, barely present in P3_12 and almost completely absent in C2. Therefore, it looks like the space group should be P1. > > However, the pseudo-procession images (attached) show clear systematic absences for 3_1 axis. Although to my untrained eyes, I cannot tell with 100% confidence about the 3-fold symmetry in the reflection intensities on the hk0 plane, even though the lattice pattern looks like 3-fold. > > Twinning test does not suggest significant twinning. > > I just don't have much experience, but assuming it is P1, is it possible for NCS to have such perfect absences? Any suggestions and comments would be much appreciated! > > Sincerely, > Chen > <CORRECT.png><hk0.png><0kl.png><h0l.png>