This sounds like a case I had last year.
It looked like P41212 (in fact I solved it by MR in P43212 and refined
the data in shelxl reasonably well. Two superimposed molecules at 50%
occupancy began to emerge from the density - this was at very high
resolution).
It took me a while to get there, but in reality it turned out to be
P212121 with TWIN 0 1 0 1 0 0 0 0 -1
I generated the new asymmetric unit (2 molecules) from the old (one
molecule) and refined from there. The improvement in R-factor was
immediately obvious with both shelxl and phenix.refine.
Hope that helps,
Cheers,
Charlie
Francis E Reyes wrote:
It seems like this space group will be the death of me.
I'm working on a structure in SG P41212 one molecule per asu that was
solved with experimental SAD phases. The resolution is to 2.5 and the
refinement is stuck at an R/Rfree of 30 and 33 with bonds rmsd of 0.011
and angles of 1.597 . The unit cell is 73.604 73.604 114.279 90.00
90.00 90.00.
I'm considering the case of perfect twinning where the real s.g. is P41
masked under the higher symmetry in P41212.
It seems to be the case in perfect twinning that the approach is to
molecular replace the refined model into the lower space group. I
reindexed my data to the lower space group P41 and molecular replaced
into the reindexed data with Phaser. A single was solution was found
with 2 mol per asu (39.6% solvent content) related by NCS.
I've refined the now two fold ncs related structure in P41 to a much
more respectable R/Rfree of 25.2 and 28.6 with rmsd bonds at 0.004 and
angles at 0.865 refining with a twin law and NCS as implemented by
phenix.refine.
However I'm not happy:
[1] a simmulated anneal omit map one of the monomers in P41 where 5
residues in a non crystal contact region of the molecule (I wanted to
challenge the omit map) shows nearly no density. (the SA OMIT map was
generated with phenix.autobuild using the same refine parameters as the
final round of refinement)
[2] the NCS selection is a little bit troubling. (maybe the phenix
developers can chime in on this)
reference = chain 'B' and (resseq 243:293 or resseq 310:370 )
selection = chain 'A' and (resseq 243:293 or resseq 310:370 )
seems as if resseq 243:293 is behaving differently than 310:370?
[3] the densities of the side chains of a helix (not an xtal contact)
are poorly defined, with geometry for the backbone not so good.
There's talk about choosing the correct MR solution (see On the
molecular-replacement problem in the presence of merohedral twinning:
structure of the N-terminal half-molecule of human lactoferrinW. A.
Breyer, R. L. Kingston, B. F. Anderson and E. N. Baker ) . I use phaser
to pick my MR solution for P41. Could phaser possibly have chosen poorly?
Thanks!
FR
---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
--
Charlie Bond
Professorial Fellow
University of Western Australia
School of Biomedical, Biomolecular and Chemical Sciences
M310
35 Stirling Highway
Crawley WA 6009
Australia
charles.b...@uwa.edu.au
+61 8 6488 4406
