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
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/
