Peter,
I had a similar case, but the centering was pseudo-I in the
monoclinic system (Oksanen et al. (2006) Acta Cryst. D62 1369-1374).
I don't think you need to delete any reflections for MR; you should
have higher than normal correlation coefficients as well as R-values.
If you see the pseudo-translation vector between the two molecules,
the solution is probably the correct one. The problem is that when
you scale your data, the error model assumes a different intensity
distribution than what you actually have. Therefore your weak
reflections will have very high sigmas and since they define the
_position_ of the molecules in the ASU, you are refining essentially
against zeros in rigid body refinement. What I did was to scale the
odd and even reflections separately, and then do rigid body
refinement against the odd (weak) and restrained refinement against
the even (strong) reflections. In the presence of significant pseudo-
symmetry, the structure is probably never going to refine very well,
at least in terms of R-value, because it is no longer a very good
indicator of structure correctness...
HTH,
Esko
Esko Oksanen, M.Sc., researcher
Macromolecular Structures Group
Research Program in Structural Biology and Biophysics
Institute of Biotechnology, University of Helsinki
Viikinkaari 1 P.O. Box 65
FIN-00014 Helsinki
FINLAND
tel. +358-9-19158953 fax +358-9-19159940
mob. +358-50-3771414
Skype ejoksane
[EMAIL PROTECTED]
On Mar 24, 2007, at 21:51, Peter J Stogios wrote:
Hello,
I posted a message about this a month ago and thanks to everyone
for their responses. At the time, I did not fully appreciate the
problem I was dealing with so this time my question is much more
specific. I would very much appreciate your help as this structure
is turning out to be very difficult to solve!
I am trying to solve a structure by MR that should be easy, given
that I have solved multiple structures of homologous proteins by
the same means. This crystal is 2.6 angstrom, apparently P212121,
with two molecules in the asymmetric unit that are related by the
pseudo-translation vector (0, 0.47, 0.5). This vector was
identified from the Patterson map, it is a peak 45% the height of
the origin peak.
As well, I have looked at all the reflection parity groups. Based
on I/sigmaI values output by Truncate, the k+l = 2n reflections are
as high as 2-fold greater in I/sigI vs. k+l = 2n+1 reflections from
16 to 5.1 angstrom. From 5.1 to 2.9 angstrom, the reverse is true:
the k+l = 2n reflections are as high as 0.62-fold LOWER in I/sigI
vs. k+l = 2n+1. Then, from 2.9 to 2.6 angstrom, each reflection
class is approximately equal in intensity.
MR using Molrep's multi-copy search, using all reflections,
consistently reproduces the pseudo-translation vector as the dyad
vector between the two molecules. However, these solutions are not
easily noticeable (Molrep just picks the highest score but this
score does not stick out from the pack), and these solutions do not
refine well via rigid body or restrained refinement in Refmac.
I have found some papers that show successful structure
determinations by MR with pseudo-translation, but I am not sure
which approach to take to solve my structure. Do I need to remove
the pseudo-weak or pseudo-strong reflections? Or do I actually use
the pseudo-weak or pseudo-strong reflections for the MR since they
will contain the information from the pseudo-translation? Which
reflections should I refine against? Should I reindex to C222 to
reflect the pseudo-face centering from the (0, 0.47, 0.5) vector?
Or am I missing something completely?
Any help would be very very much appreciated!!!! Thanks!
Peter
~
Peter J Stogios
Ph.D. candidate, Privé Lab
Dept. of Medical Biophysics, University of Toronto
Toronto Medical Discoveries Tower (TMDT) at MaRS
101 College St., Rm. 4-308
Toronto, Ontario M5G 1L7
e: [EMAIL PROTECTED]
w: http://xtal.uhnres.utoronto.ca/prive
p: (416) 581-7543
