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Dear all, Thank everyone for the insights and valuable advice! For Kay's concern, I think I do have systematic absences based on the list at the end of CORRECT.LP, but I just felt pseudo-procession images are more direct without realizing its potential pitfalls. I attached the screenshot for the list here. Pointless also suggests 151/153. And I did try MR with space group 149 / 151 / 153. The placement of target molecule is easy in all space groups. It is just the R-free and maps suggest that P1 is better than P31 and P312. I think I might have a case similar to Michael. After carefully looking at the maps. I think it might be caused by nucleic acids shared by "symmetry mates". And maybe because of the intrinsic symmetry of the duplex, the symmetry could appear to be perfect at relatively low resolution. I was just too surprised and cannot believe the absences could be so perfect for a NCS. And as Kay pointed out, I do think my phase from MR might not be good enough for solving it considering the huge gap between R and Rfree 27.4%/37.7% after refmac (P1). Thank you, Chen On Tue, Jul 19, 2016 at 5:21 PM, Mark J van Raaij <[log in to unmask]> wrote: > Although you've had some very useful advice from others, there's one more > thing I'd thought I'd mention. > As you mention radiation damage and apparently have enough data to process > in P1 (i.e. 180 degrees?), you may want to look at the R-factors per image. > If they go up significantly for the later images, perhaps discarding those > images will give you better data and a clearer answer as to what is your > spacegroup. > > Mark J van Raaij > Dpto de Estructura de Macromoleculas > Centro Nacional de Biotecnologia - CSIC > c/Darwin 3 > E-28049 Madrid, Spain > tel. (+34) 91 585 4616 > http://www.cnb.csic.es/~mjvanraaij > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.cnb.csic.es_-7Emjvanraaij&d=CwMFAg&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m=aMsM37tb93wuLzOr5CFa-L1BvLrlW4QBsMe1O8mYkIk&s=vIoGOnobfI7tot-GkU9vkcWYDiPrIotjJ-I0D1E1UOM&e=> > > On 19 Jul 2016, at 20:22, 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> > > >