I have four molecules arranged such that molecules a and b are
related by PST and adopt the same orientation as do molecules c and
d, but there is no pst between the two pairs. All molecules lie
in the same plane.
A B
top view C
D from side view / X \
I hope that the description is clear.
Any further comments would be appreciated.
Maruf
On 15 Jul 2008, at 12:28, Eleanor Dodson wrote:
One question - do you have two pairs of molecules, each related by
the PST or is there extra non-crystallographic translation ?
Averaging or NCS restraints dont give much extra information for
molecules in the same orientation.
Certainly any pseudo translation will generate sets of weak and
strong reflections but unless you have a simple fraction in each
direction it is not easy to try to select a sub-set for refinement.
Do all the data sets merge together reasonably?
You probably just have to slog it through - do you have any
experimental phasing at all?
Eleanor
Maruf Ali wrote:
Dear all
I have recently collected several datasets on different crystals
of a particular protein with a resolution range form 2.4 - 3.2A.
All datasets seem to process well in p21 with a unit cell of
109.6 83.1 115.87 90 94.8 90, and this space group is
further supported by analysis with the program pointless. The
dataset have very reasonable statistics and Rmerge values, with no
indication of twinning. Analysis of the self patterson indicated
a 43% off origin peak at 0.3 0.5 0.47. This was further
flagged by pointless and molrep as a Psuedo cell translation
(PST). Looking at the systematic absences there are some
unusually strong and weak peaks. Initially after some toiling
with molecular replacement, there was a clear solution with four
molecules in the asymmetric unit. The maps generated were good
enough to build the core of the protein but do not look like maps
generated from data at 2.4A-3.2. Further more the free R is stuck
at around 40%, and there is no difference in free R when I apply
ncs or not or any difference in the maps. After building by hand
and with phenix autobuild there is still no difference in maps and
Rfree. I have read papers where labs have successfully refined PST
data by separating the reflections according to the PST. Oksanen
et al 2006 acta D62 1369-1374: Poy et al 2001 NSMB Vol 8 no12 pg
1053: VajDos et al protein science 1997 6;2297
My specific question are
Firstly how would I deal with refining PST data? (assuming this is
the problem).
Second with off origin peak of 0.3 0.5 0.47 how would I separate
the reflections?
Thirdly any comments would be valued
Thank you in advance
Maruf
Dr Maruf Ali
Section of Structural Biology,
Institute of Cancer Research,
237 Fulham road,
London.
SW3 6JB
The Institute of Cancer Research: Royal Cancer Hospital, a
charitable Company Limited by Guarantee, Registered in England
under Company No. 534147 with its Registered Office at 123 Old
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Dr Maruf Ali
Section of Structural Biology,
Institute of Cancer Research,
237 Fulham road,
London.
SW3 6JB
The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company
Limited by Guarantee, Registered in England under Company No. 534147 with its
Registered Office at 123 Old Brompton Road, London SW7 3RP.
This e-mail message is confidential and for use by the addressee only. If the
message is received by anyone other than the addressee, please return the
message to the sender by replying to it and then delete the message from your
computer and network.
