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/
