Hello All,
I am a graduate student working on my first merohedrally twinned data set. Like
a few, I am a bit intimidated by it. After some trial and error with the help
of some online resources and ccp4bb posts, I seem to have solved the structure.
However, I am still unsure about some of the steps taken.
Background:
My dataset was processed to 1.95 A in XDS, the apparent space group is P622 (96
A, 96 A, 92 A, & 90, 90, 120). Various tests indicate that I have a twinned
dataset. The Rsym of the data when processed in a lower symmetry space group
(i.e. P6, P321 and P312) suggest that the real space group may be P6 because
its Rsym is lower by ~1-2%. The screw axis could not be unambiguously
identified from systematic absences. Molecular replacement by Phaser returned a
solution in P6(5) with 2 molecules in the asymmetric unit. This was refined in
Refmac with the twin option to R & Rfree of 22% and 25%. The twin fractions are
47% and 53%.
My questions and concerns:
- First and foremost, is there a chance that I may have processed the data in
the wrong space group (or wrongly deduced the data in the right space group)?
- Should the diffraction data be merged or unmerged during the twin refinement
in Refmac? The current dataset is fully merged (repeated measurements, Friedel
pairs & symmetry related reflections). Would there be an improvement in the
twin refinement if some of them are kept unmerged?
- Should the twin refinement be performed on the intensities or structure
factor amplitudes? I have tried both (using the same set of Rfree flags): With
intensities, the R/Rfree are 22%/25% and twin fractions are 47%/53%. With
amplitudes, the R/Rfree are 25%/29% and twin fractions are 44.6%/55.4%. The
resulting electron density maps are not significantly different, however. I
don't understand why the statistics vary so significantly.
- During the model building, the electron density map appears to be 'weak'.
Rebuilding some surface loops (by first deleting them, refining the omit
structure, and remodeling into the difference map) which initially has some
2Fo-Fc density becomes tricky because there is not much density left in the
refined omit structure. Was the initial densities purely a result of model bias
or is this related to the twinning of the crystal? Could this also be because
Refmac outputs a differently weighed 2Fo-Fc map (if I recall correctly) during
twin refinement?
I would be very grateful for any help, comments and suggestions.
Best,
Peter Chan
