Rwork = 0.26 and Rfree = 0.32 are not necessarily unacceptably high
for a 2.3 A dataset in my opinion.
Not all crystals are the same, some just have more disorder than
others and not all of this disorder is modelable (if that is a word).
Having said that:
- is the 2.3A data cutoff perhaps a tad optimistic and is your
structure really more like 2.5-2.7A?
- have you correctly modelled solvent/ions etc.?
- did you try TLS analysis and refinement?
- is yours a protein/DNA complex? I understand they often have a
higher R-factors, the specialists may contribute their opinions on the
reason (disorder in DNA? restraints for nucleic acids being less good
than for protein?).
From the information you give, I think you can be confident about the
P21212 spacegroup.
Mark
Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/
researcherID: B-3678-2009
On 3 Dec 2009, at 18:49, Robert Radford wrote:
Hello-
I am working up a data that is giving me unacceptable high R factors.
I am solving a data set that is good to ~ 2.3 Å using molecular
replacement based on a previously crystalized variant. The maps look
good with all the density fitting well to my model. I originally
worked up the data using PHASER for the molecular replacement. It
searched all alternative orthorhombic space groups and found a
single solution in P2(1)2(1)2 but that only gave me final R factors
of (Rwork = 0.26 and Rfree = 0.32) Next I went back and tried to
work the data up in a different space group. Thus far I have tried
P21 and P1. Both these space groups give me essential the same final
statistics (~Rwork = 0.26 and Rfree = 0.32). Furthermore, the
solution looks the same, the only change being the number for
monomers in the asymmetric unit (1, 2, 4 for P21212, P21 and P1
respectively) The diagnostics don't indicate that the crystal is
twined and the data set looks good (i.e. the spots are nice and well
separated)
The unit cell dimensions for the three cases as
P1: a = 34.55 b = 46.95 c = 88.56, alpha = 89.94, beta = 90.03
gamma = 89.99
P21: a = 46.91 b = 34.52 c = 88.47, alpha = 90 , beta = 90.03
gamma = 90.0
P21212 a = 88.44 b = 34.51 c = 46.89, alpha = 90.0, beta = 90.00
gamma = 90.0
One possible complication is that the biological unit is dimeric
with 2 fold symmetry. The 2 fold symmetry axis for the protein
appears to be sitting on a 2-fold crystallographic axis.
Any suggestions?
Thank you in advance.
Robert
________________
Robert Radford
Graduate Researcher
Dept. Of Chemistry
UC San Diego
