Your suspiciously low spread between R and Rfree might be because your
free flags might not have been chosen considering the twinning law.
Twin-related reflections should have the same flag value. You can get
phenix's reflection file utility to pick free flags for you while taking
the twinning law in consideration, or you can downgrade the symmetry of
your P422 data to P222 while keeping the free flags. You'll have to
either shake your cordinates or do simulated annealing to get rid of the
memory of the flag in your model.
Engin
On 6/22/09 6:16 PM, Brett Collins wrote:
Dear all,
I posted here recently regarding a potential twinning problem I had
and got some very useful feedback.
The summary of what happened is I had a crystal that appeared to be
P42212 from systematic absences after scaling in SCALA (a,b,c;
118,118,192). Interestingly POINTLESS suggested P41212 (or P43212 as
the best solutions), and PHASER could only find a solution in P41212
(2 mol/asu). Cumulative intensity plots suggested twinning, as did
phenix.xtriage, and refinement at 2.6 A resolution was stuck at
R/Rfree of 25.5/32.0. (Rmerge 6.5%). Although people suggested using
refmac with twin refinement, in P41212 no twin laws were identified in
REFMAC or phenix.xtriage.
I tried indexing in lower symmetry P222 (a,b,c; 118,118,192) (Rmerge
5.4 %). PHASER found a solution in p212121 (4 mol/asu). Refinement now
proceeds to R/Rfree of 25.3/27.9.
I tried additional twin refinement in in P212121 using REFMAC, which
found the twin operator k,h,-l with fraction ~43%. However, R/Rfree
only changed marginally (and suspiciously) to 25.6/26.9.
Importantly, in each case the maps seem good and I can't discern any
significant difference between them.
My questions are
(i) which (if any) solution should I trust?
(ii) Is the drop in R factors in p212121 just because parameters/data
ratio is less? i.e Am I just overfitting the data?
(iii) Do I really have twinning?
Cheers,
Brett
################################
Brett Collins, PhD
Group leader
Institute for Molecular Bioscience
Level 3 North
Queensland Bioscience Precinct
The University of Queensland
St. Lucia, 4072, Qld,
AUSTRALIA
e-mail: [email protected] <mailto:[email protected]>
phone: 61-7-3346-2043
FAX: 61-7-3346-2101
website: http://www.imb.uq.edu.au/index.html?page=82433
Courier address:
Institute for Molecular Bioscience
Queensland Bioscience Precinct
Building 80, Services Road
University of Queensland
St. Lucia, Brisbane
Queensland, Australia 4072
################################
--
Engin Özkan
Post-doctoral Scholar
Laboratory of K. Christopher Garcia
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111
