Hi Maruf,
1) Why the low-resolution data was collected to 3.2 Å?
2) Is it possible the real space group is P2 with a NCS which making
it look like P21, especially when the PST has a value of exact 0.5.
Lijun
On Jul 14, 2008, at 5:42 AM, 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
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Lijun Liu, PhD
Institute of Molecular Biology
HHMI & Department of Physics
University of Oregon
Eugene, OR 97403
541-346-4080
