Points to think about.
1) Do your data statistics indicate twinning - if they dont iyt is mst
unlikely to be present
Look at output of truncate ( new Ctruncate is better)
Get phenix xtriage report..
2) SAD phasing - I presume you knw it is P41212 and not P43212?
3) Going to a lower symmetry.
You dont need to rerun MR - just keep the molecule where it is and
generatea second using symmetry operator y,x,-z
4) Are you doing twinned refinement? If so the Rfactors are not really
comparable..
Best test is? Do the maps look better.
It is easy to compare them using COOT providing you have kept the same
origin for the P41 and P41212 solutions.
Eleanor
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
