Hey Stephen,
how about simply putting three models, separated by 16A, into your
original unit cell and refining them together. You'd have to guess
their fractional occupancies from the heights of the Patterson peaks
(and make them add up to one, obviously).
This approach (in contrast to correcting the intensities) was the
consensus when I talked to Peter Zwart and Tom Terwilliger about a
similar problem. As my problem still hasn't been solved (probably
because of flawed data processing due to overlapping spots), I'd be very
keen on hearing about your progress.
http://scripts.iucr.org/cgi-bin/paper?S0907444908016648
describes both approaches to lattice-translocated crystals (correcting
intensities and refining several models concurrently).
http://scripts.iucr.org/cgi-bin/paper?ba5111
is the best review on the subject.
All the best.
Andreas
Stephen Hare wrote:
Dear All,
We are currently working on a structure of apparent P21 symmetry which
has been solved by molecular replacement. The data are to 2.7Å but the
Rfree will not drop below 30%. The density is clear for the model we
have, however there is extra density that suggests a shift of the
structure by 16Å in either direction - resulting in three possible
overlapping positions for the structure. We assume this is the result of
twinning.
The unit cell dimensions are 102.7Å, 83.0Å, 115.3Å, 90°, 101.8°, 90°.
Examining the data with phenix.xtriage also suggests pseudo
translational symmetry with a separation of 16Å. A Patterson peak at
0.097, 0.000, -0.096 is approximately 30% of the origin peak, while a
second peak of double the translation at 0.192, 0.000, 0.195 is 7% of
the origin peak. The structure contains a dimer of dimers with an NCS 2
fold axis almost perpendicular to the crystallographic 2 fold. This NCS
axis almost coincides with the diagonal between the A and C axes. A
twin axis along the A C diagonal (l,-k,h) could explain the observed
extra density, however this is not possible because A and C are
different lengths.
As a result of the NCS axis running almost perpendicular to the observed
P21 axis, it is possible to merge the reflections in a larger
orthorhombic unit cell - dimensions 137.1Å, 83.3Å, 169.8Å although here
the Rmerge is higher and it is not possible to get a molecular
replacement solution.
Is it possible to define the (l,-k,h) twinning operator in our original
unit cell? or have we missed the actual unit cell? Or....something else?
Steve
Stephen Hare PhD
Post doctoral research associate
Jefferiss Research Laboratories
Wright-Fleming Institute
Division of Medicine
Imperial College London
Norfolk Place
London W2 1PG
UK
Phone: +44 (0) 20 7594 3908
Fax: +44 (0) 20 7594 3906
--
Andreas Förster, Research Associate
Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
