Yes, the data indeed seems to be twinned and the tNCS has masked the twinning statistics, which is why I haven't considered it so far.
I have not tried twinned refinement in C2 and P1 yet, but refining 4 chains in P32 with twinning yields a difference ED map that clearly indicates one (and just on!) orientation for the 5th chain. Thank you all for your suggestions. Have a nice evening, Peer -----"CCP4 bulletin board" <CCP4BB@JISCMAIL.AC.UK> schrieb: ----- An: CCP4BB@JISCMAIL.AC.UK Von: "Kay Diederichs" Gesendet von: "CCP4 bulletin board" Datum: 26.08.2021 16:41 Betreff: Re: [ccp4bb] chain on 2-fold axis? Dear Peer, I suspect that the true spacegroup has lower symmetry than P3221, and that there may be twinning masked by tNCS. Subgroups of P3221 are C2 and P32 ( https://strucbio.biologie.unikonstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups ) and of course P1. What I'd do is process the data, and solve (use the best chain of the refined P3221 model for MR) and refine the structure in these spacegroups. Inspect the results: If P1 is clearly better than P32 and C2, P1 is correct. If C2 (P32) is clearly better than P32 (C2), then P1 should give the same R-values as the better one; if so, P1 can be discarded. Try this with and without twin refinement - although it's hard to compare R-values of non-twinned and twinned refinements. The automatic way to do this is with Zanuda. If you run that locally, you can make refmac do twin refinement. For all resulting structures, I'd also feed the resulting Fcalc (!) into pointless. That should reveal that the packing is indeed close to P3221. Best wishes, Kay On Thu, 26 Aug 2021 11:54:06 +0200, Peer Mittl <mi...@bioc.uzh.ch> wrote: >Der CCP4 community, > >Is there a refinement program that can handle protein monomers sitting >on crystallographic 2-folds? > >This is probably a strange question but we have the following situation. >We have a 2.6 Ang datasets in SG P3221 (Rpim=4%, Isa=19.6) and a clear >molrep solution with 2 chains, albeit with tNCS (0/0/0.5) that can be >refined to around 27/33% Rfactor. According to Vm a third chain could be >present. So far so good, but there is clear difference ED for a third >chain sitting exactly on the 2-fold. Since the protein has a peculiar >shape, one can tell even its orientation. I can relax the symmetry to >P32 (or even P1) and place the missing chain with 50% occupancy on the >2-fold. This model can be refined, but I do not like this work around, >because the data is clearly P3221. > >Any hints on similar crystal pathologies and how they have been handled >would be helpful. > >All the best, >Peer > >######################################################################## > >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/ ######################################################################## 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/
