Yes re resolution. The AIMLESS report will suggest a sensible resolution limit based on I/SigI and CChalf, and it is sensible to reprocess the data using that cut off. One of my favorite checks is the REFMAC Rfactor v resolution plot - if the Rfactor rises steeply you probably are getting no advantage from the high resolution.. Eleanor
On Fri, 17 Jul 2026 at 15:38, John Bacik < [email protected]> wrote: > Another possibility is that the data was processed to an unreasonably high > resolution. So for example, if the diffraction extends to 2.4A with > reasonable statistics, but processed to 1.8A, then resulting refinement > R-values will be higher than expected. > > All the best, > John > > On Friday, July 17, 2026 at 08:56:45 AM CDT, Kay Diederichs < > [email protected]> wrote: > > > Now I realize that I did not answer your question why the R-values are > higher than expected for a 1.8A structure near the end of the refinement. > It could be > - not indexing (say) half of the reflections because they are > systematically weak due to tNCS, resulting in wrong (too small) cell > parameters > - wrong spacegroup (you should check the other two P21 settings, and P1) > - twinning of a P1 or P21 crystal that happens to have all-90° angles > - strong anisotropy showing 1.8A only in one or two directions, but much > less into the other(s). > - translational NCS producing higher-than-normal R-values because (say) > half of the reflections is weak > - several crystals in the loop whose diffraction patterns overlap, thus > distorting the intensities > - other kinds of disorder (rare) > - model not accounting for all atoms in the ASU, or wrong chain > tracing/sequence/register; is the density satisfactory? > > Probably I forgot something ... > > As Eleanor said: inspect at least post the pointless logfile, and the > scaling statistics, and the anisotropy information from PHASER, and maybe > post that here. > > Best, > Kay > > > On Fri, 17 Jul 2026 11:02:44 +0100, Eleanor Dodson < > [email protected]> wrote: > > >I guess you must have CCP4 software installed? > >Try setting up a project with CCP4I2 and running the task under > >Xray data reduction and analysis > > Data reduction - AIMLESS > > > >This will give you a detailed report on possible spacegroups and > indexing.. > >Very helpful for a beginner! > > > > > >On Fri, 17 Jul 2026 at 08:03, Kay Diederichs < > >[email protected]> wrote: > > > >> Hello Jakob, > >> > >> The highest-possible crystal symmetry should always be used, in order to > >> make the description of the experiment as simple (parsimonious) as > possible. > >> > >> In my book, the R-values you report are the "same" for P21 and P212121 > >> ("same" meaning "similar enough to be explained by different choice of > free > >> reflections, and different degrees of freedom resulting from having > twice > >> as many atoms"). That means that the higher symmetry is the correct one. > >> > >> Just note that you can _always_ refine in a lower-symmetry subgroup, > >> without really changing the scientific insight from the experiment. > >> P21 is a subgroup of P212121. Note that in your case, you can choose the > >> unique axis of P21 in three ways - you chose one of them. The other two > >> should give similar R-values. > >> You could even refine in P1 (of course with 4 times the number of > >> molecules in the ASU, compared to P212121, and twice compared to P21), > >> without significantly changing the R-values. > >> > >> Hope this helps, > >> Kay > >> > >> ######################################################################## > >> > >> 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/ > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## 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/
