As you say the operator h,-h-k,-l ( equivalent to k,h,-l) is a symm op
for P3121.
However there is another possible twinning operator -h,-k,l in P3121
which you should check out.
( see http://www.ccp4.ac.uk/dist/html/twinning.html for possible twin
operators)
This doesnt explain your poor agreement between reflection related by
the 3-fold symmetry though.. Either the symmetry is lower t han you
think. (unlikely since it processes quite well for the majority of the
data, or there is an absorbtion/integration problem
Eleanor
jess v wrote:
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Hi,
I’ve collected multiple datasets (MAD and native) on crystals with
apparent trigonal symmetry and am having trouble refining my model.
The data scales reasonably well in both P31 and P3121. The data are
highly mosaic (typically 1.5-1.8), and though the # rejects is
reasonable, the rejections of some reflections look suspicious
(below). I was eventually able to phase my MAD data using the
protein-bound 4Fe4S cluster (in P31, 2molec/ASU=40%solvent; in P3121,
1molec/ASU=40% solvent, both consistent with the experimental electron
density) and with the exception of a ~10-residue disordered loop,
built most of the protein backbone and ~40% of the sidechains.
Refinement of my model in CNS and SHELXL yields highly divergent or
very high (>40) Rfactors in both space groups.
The obvious possibility is twinning. I ran the data (processed in P31)
through the Yeates server, which showed an intensity distribution that
did not indicate twinning, but gave results to the partial twinning
test that suggested near-perfect twinning with the operator h, -h-k,
-l. I think this may be an artifact of actual higher symmetry, but
when I refined in SHELXL with the suggested operator and twin
fraction, in P31 with two molecules, my Rs dropped to 28 and 34 (at
best), but won't improve further.
I’m not quite sure how to proceed from here. I’ve tried improving the
data quality by reprocessing my natives, annealing / improving the
crystals to get one with lower mosaicity, refining in different space
groups. I’ve had trouble obtaining other crystals forms that diffract,
so any input on how to salvage this data would be much appreciated.
Thanks,
Jess
In P3121:
8 -2 18 102.4 1342.3 4.75
8 -2 18 a+ 35 0.8 827.5 0 168.1
-2 -6 18 a+ 109 11.2 2072.8 100 170.7
-2 8 -18 a+ 77 6.1 1447.6 100 167.9
-6 -2 -18 a+ 4 -1.1 656.7 0 165.4
-8 2 -18 a- 23 0.5 792.0 0 166.3
2 6 -18 a- 88 8.9 1784.6 100 169.9
2 -8 18 a- 92 8.6 1752.6 100 170.0
6 2 18 a- 16 -0.1 739.9 0 166.1
-8 6 18 a- 110 11.7 2106.2 100 169.1
In P31:
11 -6 13 42.2 1506.3 4.54
11 -6 13 a+ 53 0.0 939.7 0 190.2
-5 11 13 a+ 126 5.5 1843.7 100 199.7
-11 6 -13 a- 41 -0.1 929.4 0 188.8
6 5 -13 a- 127 9.1 2411.9 100 196.8
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