Hi Sabine,
If your question is: Is it possible to refine twinned structures with
Refmac?
My answer is: Yes. Very well.
Best wishes,
Roberto
On 20 Feb 2009, at 16:32, Sabine Schneider wrote:
Hi everyone,
I got good data to 2.4A on a protein-ligand complex. I want to
solve the
structure by MR using a model with 45% seq. ID and 55% similarity.
Initially the data appeared to be P622 (pointless, selfrotation
function
etc). Unit cell: 145 145 65, MW protein is 28kDa
I prepared the MR model with chainsaw, choping of non-conserved
residues
at the C gamma and reset the B-factors. Phaser found a solution, but
with negativ LLG.
I than processed the data in P3, P321, P312 and P6 and run Phaser
searching all possible alternative spacegroups. The best solution
is P3
(4mol/asu) followed by P321 (2mol/asu),both with a LLG of above
400. But
when trying to refine the models in Refmac the R/Rfree stays at ~48%.
Looking at the truncate output and phenix xtriage, twinning is
suggested
with the merohedral twin law -h, -k, l and a twin fraction of 40.3%
Using twin refine option in Refmac (5.5.0070), the R/Rfree for the
P321
solution drops to around 33%, but the difference between R/Rfree is
only
1%. For the solution found in P3 the R/Rfree stays at around 47%.
So I assumed that P321 is the better solution. Is the difference in
R/Rfree only 1%, because the free and work reflections are related
through the twin law?
I used phenix to assign the free reflections putting in the twin
operators. Doing simulated annealing in phenix, I get a rather large
difference in R/Rfree of ~7%. Well, I guess I need to do some
tweaking
of the parameters in phenix (running the latest phenix and cci_apps).
When I than use these free reflections assigned by phenix in Refmac I
still get only 1.5% difference between R and Rfree?
So is it doable in Refmac, or is my best bet phenix? Any advice
what is
the best way to proceed is much appreciated!
Sabine
------------------------------------------
Dr. Sabine Schneider
Ludwig-Maximilians-University
Department of Chemistry and Pharmacy
Butenandtstrasse 5-13, Building F
81377 Munich
Germany
Phone: +49 (0)89 2180 77846
Fax: +49 (0)89 2180 77756
http://www.carellgroup.de/
---
Roberto Steiner
Randall Division of Cell and Molecular Biophysics
New Hunt's House
King's College London
Guy's Campus
London, SE1 1UL
Phone +44 (0)20-7848-8216
Fax +44 (0)20-7848-6435
e-mail roberto.stei...@kcl.ac.uk
