It’s difficult to tell exactly what is happening from your description and the attached image. Both your description and the image are OK. It’s just that there are a lot of ways for things to go off the rails.
Are the molecules stacked end-to-end? In that case, you may have an incommensurate structure where the molecule is disordered around a pseudo-continuous helical axis running through the crystal. But from this view, it looks like at least two bases are swung out to the left. I’d omit the interaction region, refine what you can model well as well as you can, and see if the maps for this region clear up. Keep in mind that your model might be out of register, so look at the shapes of the bases carefully to see if you need adjust that. On Jun 8, 2021, at 10:14 AM, [email protected]<mailto:[email protected]> wrote: Hello everyone, I am working with an RNA-only structure, data are at 3 Angstroms, and at first, I thought was in the C2 space group (with 6 molecules in the AU). I can't finish building! it, because the structure seems to get in the way of its neighbor symmetrically! See the attached picture, please! The only 4 residues that the structure is missing "have to go there", where one structure meets the other one. The R factors for this spacegroup are around 0.3. However, Phenix Xtriage suggests the symmetry may be higher. So I reindex in P622, do MR with Phaser (trying all possible space groups in that point group), and it finds a unique solution in space group P 65 2 2 with TFZ of 50 and LLG >3000. Of course, the problem persists (one molecule sort of interfering with the neighbor), not only that but also the refinement R-factors are substantially higher, 0.37. I have to say that the refinement maps look better when I am working with the C2 spacegroup. I can't understand, though, what is happening at that "supposedly interface" between the two molecules. Has anybody experienced anything like this in the past? Can it be a twin? Is it something else? and... how to fix it? Thank you very much in advance. Best wishes, Almudena ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <Screenshot 2021-06-08 at 16.42.54.png><Screenshot 2021-06-08 at 16.43.21.png><Screenshot 2021-06-08 at 16.43.38.png> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
