Hi Petr,
Usually IDXREF suggests more than one Bravais lattice that is consistent
with your diffraction images;
hence it is (sometimes) worthwhile trying to INTEGRATE in all possible
Bravais lattices and this allows you to eliminate a number of
possibilities (poor profiles during integration, instability of
refinement, poor Rmerge values at the level of CORRECT). This leaves you
with a smaller number of choices for the Bravais lattive. And I
personally (at the end) integrate in the correct Bravais lattice instead
of integrating in P1 and then doing the space group assignment at the
level of CORRECT. I get improved Rmerge values then.
I've had a case where one of the students here was wrongly advising my
student about an orthorhombic space group, and my advice to carry out
integration in all Bravais lattices suggested by IDXREF, integration led
in orthorhombic gave a molecular replacement solution that did not
refine properly and a molecular replacement solution that refined in a
hexagonal space group. The Rmerge values (at the level of CORRECT) vere
very similar both for P222 and for P6 integration.
HTH,
Fred.
Petr Kolenko wrote:
Dear colleagues,
I appreciate any help, or any suggestion with my difficult data. Many
thanks at least for consideration.
I work with datasets at 3.6AA of resolution. Integrated with XDS,
scaled with SCALA. After integration and scaling in P1, POINTLESS
suggested space group I432:
Space group confidence: 0.95
Laue group confidence: 1.000
Total probability: 0.97
After any longer refinement (more than 20 cycles), there was always a
big gap between Rwork and Rfree (0.22 and 0.33), although the
structure looks quite good at this resolution. I tried also space
group I23, here are my statistics:
Data processing (I23 vs I432):
Rmerge - 0.124 vs 0.134
high resolution Rmerge - 0.649 vs 0.732
low resolution Rmerge - 0.048 vs 0.037
The gap between Rwork and Rfree was stabilized in I23 using tight NCS
restraints:
Rwork vs Rfree:
I23 withouth NCS: 0.228 vs 0.334
I23 with NCS: 0.249 vs 0.296
I43 : 0.228 vs 0.326
My question is, what would you recommend me to close the gap? Or is
this Rfree pointing out a lower real symmetry (I23) than suggested by
POINTLESS or PHENIX.XTRIAGE (I432)? I have tried different selection
of free reflections in I432 dataset already, but with almost the same
results.
Many thanks for any response.
Petr
