Dear Peer and Eleanor, This is indeed what I am suspecting: If the "twinning operator" in P32 puts 4 out of 5 protein chains on top of symmetry mates, is the "true" space group then P32, with 5 twinned chains, or P3221 with 4 normal chains and 1 chain on a special position? I would vote for the latter.
Best, Herman Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Peer Mittl Gesendet: Freitag, 27. August 2021 10:17 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis? Dear Eleanor, I indeed used r/tefmac for the refinement and it came up with the values HKL (a=0.56), KH-L (a=0.44). It would be interesting to see if a refinement in P3221 would come up with the same occupancies for the alternative conformations for the "extra" chain on the 2-fold axis. It seems as if the "well-ordered" chains (2 in P3221, 4 in P32) form a sublattice with P3221 symmetry and it's just the "extra" chain, which generates the twinning. All the best, Peer On 26.08.2021 18:09, Eleanor Dodson wrote: > Motto =mitti in predictive text! > > On Thu, 26 Aug 2021 at 16:52, Eleanor Dodson > <eleanor.dod...@york.ac.uk > <mailto:eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk%20%3cmailto:eleanor.dod...@york.ac.uk>>> > wrote: > > Great, motto. I think you have nailed it! Did you use tefmac for > twinned refinement? And if so what did it suggest the twin > fraction is? > > On Thu, 26 Aug 2021 at 16:30, Peer Mittl <mi...@bioc.uzh.ch <mailto:mi...@bioc.uzh.ch%0b>> <mailto:mi...@bioc.uzh.ch>> wrote: > > 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 <mailto:CCP4BB@JISCMAIL.AC.UK%0b>> <mailto:CCP4BB@JISCMAIL.AC.UK>> schrieb: ----- > An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> > <mailto: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<https://strucbio.biologie.unikonstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups> > <https://strucbio.biologie.unikonstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups<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 > <mailto:mi...@bioc.uzh.ch<mailto:mi...@bioc.uzh.ch%20%3cmailto: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<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<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<http://www.jiscmail.ac.uk/CCP4BB> > <http://www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>>, > a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk> > <http://www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>>, terms & conditions > are available > at > https://www.jiscmail.ac.uk/policyandsecurity/<https://www.jiscmail.ac.uk/policyandsecurity> > <https://www.jiscmail.ac.uk/policyandsecurity/<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<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<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<http://www.jiscmail.ac.uk/CCP4BB> > <http://www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>>, > a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk> > <http://www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>>, terms & conditions > are available > at > https://www.jiscmail.ac.uk/policyandsecurity/<https://www.jiscmail.ac.uk/policyandsecurity/> > <https://www.jiscmail.ac.uk/policyandsecurity/<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<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<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<http://www.jiscmail.ac.uk/CCP4BB> > <http://www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>>, > a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk> > <http://www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>>, terms & conditions > are available > at > https://www.jiscmail.ac.uk/policyandsecurity/<https://www.jiscmail.ac.uk/policyandsecurity/> > <https://www.jiscmail.ac.uk/policyandsecurity/<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<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>> > -- **************************** Peer Mittl, PD Dr. Biochemisches Institut Universität Zürich Room 44M03 Winterthurer Strasse 190 CH-8057 Zürich Tel. +41-(0)44-6356559 Mobile +41-(0)76-2776566 Fax. +41-(0)44-6356805 Mail mi...@bioc.uzh.ch<mailto:mi...@bioc.uzh.ch> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/<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/
