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 Brompton Road, London SW7 3RP.
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