Hi Almudena, if it is a packing problem, you need to find the correct subgroup of P6522 (179). Take a look at https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups . Subgroups of 179 are 20, 153, 154, 170, and recursively each of these has subgroups: 20 has 4 and 5 as subgroups, 153 and 154 both have 5 and 145 as subgroups, 170 has 4 and 145 as subgroups - taken together, 4, 5 and 145. These have 1 as subgroup. So the true space group could be P1, P21, C2, P32, C2221, P3212, P3221, P65. You could run molecular replacement with all of these. Unfortunately, there may be several ways to index the data in some of these space groups, and they may not be equivalent. For example, I think there are 3 non-equivalent ways to index in C2 or P21 if the Laue class is 6/m .
If there is twinning, the intensity statistics should tell about that - but they may be set off by tNCS. One way to overcome the mess of possible space groups and settings plus the twinning possibility is to index and solve the structure in P1. That should allow a packing without clashes, and one could identify the correct space group by running POINTLESS on the Fcalc, and/or Zanuda. Since you have a good model, I'd try that. Hope this helps, Kay On Tue, 8 Jun 2021 17:14:30 +0200, Almudena Ponce Salvatierra <[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 > >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/ > ######################################################################## 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/
