I am working on a structure that is twinned (merohedral) in P41. Initial estimates of twinning fraction (via xtriage and Yeates server) are around 0.37; in refinement they start around 0.49 and drop to 0.46 (so far).
One can compensate for 'model imperfection' by inflating the twin fraction: in the early stages of refinement the twin fraction might be seomwhat higher due to this reason.
I should mention that data processing wasn't easy- this crystal form also has an apparent epitaxial twin in the b dimension causing a doubling in that dimension. During indexing (with SAINT) I applied a transformation of 100 00.50 001 to the reflections, which then gave me the expected cell and from
What about a? Are you sure that you don't have pseudo translational symmetry somehow?
Xprep the data looks OK. (Yes, I am trying to grow different forms) Maps look nice, although I wish my ligand had more/better density.
When twin fractions are highish, density can be rather biased. This also means that when you don't place model atoms in a certain area, you tend not to see density there.
I ran phenix.refine with defaults, and included twin_law="h,-k,-l", xray_data.r_free_flags.generate=true, detwin.map_types.aniso_correct=true and also simulated_annealing=true. My starting R/ Rfree is 0.448/ 0.4385; ending is 0.2962/ 0.4270. Geometry is somewhat tighter after refinement but is better (bonds 0.017 to 0.01, angles 1.966 to 1.530). I have not included my ligand, and I can see a few spots where the model needs adjusting, but nothing majorly wrong.
Did you try using TLS?
Why is my Rfree hanging so high? Is it becaues I have bad karma?
Future bad karma can be avoided by refining without attachment.
Is it to do with the twinning? I am pretty sure my space group is right (based on the above info and the maps look fine; Phaser could not find a solution in P43). There isn't room for anything else in the cell.
I would try TLS and recheck the unit cell parameters. P
Any opinions or suggestions are most welcome as I wait for better xtals to grow... Thanks in advance, Christina
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