Dear all,
I have some troublesome data to ~2.3A and I hope someone can help. My data
indexes and scales equally well in I222, C2 and P1
I222 a=46.3 b=76.3 c=81.1
C2 a=111.3 b=46.3 c=76.3 beta=133.2 (reset in I2 a=76.3 b=46.3 c=81.1
beta=90.1)
C2 a=94.5 b=76.3 c=46.3 beta=119.6 (reset in I2 a=46.3 b=76.3 c=81.1
beta=90.1)
P1 a=46.2 b=60.2 c=60.2 alpha=78.5 beta=67.4 gamma=67.4
I have found a molecular replacement solution in I212121 using an NMR structure
of the same protein and MR-ROSETTA/PHENIX (PHASER LLG=128 TFZ=12.3), although I
can not refine this below R ~45% and Rfree ~50%. The maps look OK in parts but
in other regions the connectivity is much reduced. In case of model bias I have
used density modification and also used simulated annealing etc in case it is
stuck in a local minima - these did not help. This protein is an Ig-like fold
(potential for pseudo-internal symmetry) and so I have also played around with
rotations of the structure but this has not helped. Although twinning analysis
in all spacegroups suggest there is no twinning I have tried refinement in
PHENIX and REFMAC using twin laws but this does not help.
I do not detect any off origin peaks in a native Patterson map but I do see
peaks suggesting NCS in self rotations in I222 (see below for peaks above 50%
origin) - there can only be 1 mol/au though. Does this suggest rotational
lattice defects?
Eulerian angles Polar angles
Alpha Beta Gamma Peak Omega Phi Kappa
Direction cosines
Symmetry: 1 2
Peak 1
Origin peak 100.0 0.0 0.0 0.0
Peak 2
1 1 0.0 0.0 180.0 100.0 0.0 0.0 3.1
0.0000 0.0000 1.0000
Origin peak 100.0 0.0 0.0 180.0
Peak 3
1 1 0.0 0.0 180.0 100.0 0.0 0.0 3.1
0.0000 0.0000 1.0000
Origin peak 100.0 180.0 0.0 180.0
Peak 4
1 1 0.0 180.0 180.0 100.0 90.0 0.0 3.1
1.0000 0.0000 0.0000
1 2 0.0 180.0 0.0 100.0 90.0 90.0 3.1
0.0000 1.0000 0.0000
Origin peak 100.0 90.0 0.0 180.0
Peak 5
1 1 0.0 180.0 180.0 100.0 90.0 0.0 3.1
1.0000 0.0000 0.0000
1 2 0.0 180.0 0.0 100.0 90.0 90.0 3.1
0.0000 1.0000 0.0000
Origin peak 100.0 90.0 180.0 180.0
Peak 6
1 1 0.0 180.0 0.0 100.0 90.0 90.0 3.1
0.0000 1.0000 0.0000
1 2 0.0 180.0 180.0 100.0 90.0 0.0 3.1
1.0000 0.0000 0.0000
1 3 0.0 0.0 180.0 100.0 0.0 0.0 3.1
0.0000 0.0000 1.0000
Origin peak 100.0 90.0 90.0 180.0
Peak 7
1 1 270.0 89.9 90.0 51.9 90.0 0.0 89.9
1.0000 0.0000 0.0000
1 2 270.0 89.9 270.0 51.9 45.0 270.0 180.0
0.0000 -0.7067 0.7075
1 3 90.0 90.1 270.0 51.9 90.0 180.0 90.1
-1.0000 0.0000 0.0000
1 4 90.0 90.1 90.0 51.9 135.0 270.0 180.0
0.0000 -0.7075 -0.7067
2 1 90.0 89.9 90.0 51.9 135.0 270.0 180.0
0.0000 -0.7067 -0.7075
2 2 90.0 89.9 270.0 51.9 90.0 180.0 89.9
-1.0000 0.0000 0.0000
2 3 270.0 90.1 270.0 51.9 135.0 90.0 180.0
0.0000 0.7075 -0.7067
2 4 270.0 90.1 90.0 51.9 90.0 360.0 90.1
1.0000 0.0000 0.0000
3 1 90.0 90.1 270.0 51.9 90.0 180.0 90.1
-1.0000 0.0000 0.0000
3 2 90.0 90.1 90.0 51.9 45.0 90.0 180.0
0.0000 0.7075 0.7067
3 3 270.0 89.9 90.0 51.9 90.0 360.0 89.9
1.0000 0.0000 0.0000
3 4 270.0 89.9 270.0 51.9 135.0 90.0 180.0
0.0000 0.7067 -0.7075
4 1 270.0 90.1 270.0 51.9 45.0 270.0 180.0
0.0000 -0.7075 0.7067
4 2 270.0 90.1 90.0 51.9 90.0 360.0 90.1
1.0000 0.0000 0.0000
4 3 90.0 89.9 90.0 51.9 135.0 270.0 180.0
0.0000 -0.7067 -0.7075
4 4 90.0 89.9 270.0 51.9 90.0 180.0 89.9
-1.0000 0.0000 0.0000
Peak 8
1 1 90.0 89.9 270.0 51.9 90.0 180.0 89.9
-1.0000 0.0000 0.0000
1 2 90.0 89.9 90.0 51.9 135.0 270.0 180.0
0.0000 -0.7067 -0.7075
1 3 270.0 90.1 90.0 51.9 90.0 360.0 90.1
1.0000 0.0000 0.0000
1 4 270.0 90.1 270.0 51.9 135.0 90.0 180.0
0.0000 0.7075 -0.7067
2 1 270.0 89.9 270.0 51.9 45.0 270.0 180.0
0.0000 -0.7067 0.7075
2 2 270.0 89.9 90.0 51.9 90.0 360.0 89.9
1.0000 0.0000 0.0000
2 3 90.0 90.1 90.0 51.9 45.0 90.0 180.0
0.0000 0.7075 0.7067
2 4 90.0 90.1 270.0 51.9 90.0 180.0 90.1
-1.0000 0.0000 0.0000
3 1 270.0 90.1 90.0 51.9 90.0 360.0 90.1
1.0000 0.0000 0.0000
3 2 270.0 90.1 270.0 51.9 45.0 270.0 180.0
0.0000 -0.7075 0.7067
3 3 90.0 89.9 270.0 51.9 90.0 180.0 89.9
-1.0000 0.0000 0.0000
3 4 90.0 89.9 90.0 51.9 135.0 270.0 180.0
0.0000 -0.7067 -0.7075
4 1 90.0 90.1 90.0 51.9 45.0 90.0 180.0
0.0000 0.7075 0.7067
4 2 90.0 90.1 270.0 51.9 90.0 180.0 90.1
-1.0000 0.0000 0.0000
4 3 270.0 89.9 270.0 51.9 135.0 90.0 180.0
0.0000 0.7067 -0.7075
4 4 270.0 89.9 90.0 51.9 90.0 360.0 89.9
1.0000 0.0000 0.0000
Peak 9
1 1 90.0 90.0 90.0 51.5 135.0 270.0 180.0
0.0000 -0.7072 -0.7070
1 2 90.0 90.0 270.0 51.5 90.0 180.0 90.0
-1.0000 0.0000 0.0000
1 3 270.0 90.0 270.0 51.5 45.0 270.0 180.0
0.0000 -0.7070 0.7072
1 4 270.0 90.0 90.0 51.5 90.0 0.0 90.0
1.0000 0.0000 0.0000
2 1 270.0 90.0 90.0 51.5 90.0 360.0 90.0
1.0000 0.0000 0.0000
2 2 270.0 90.0 270.0 51.5 135.0 90.0 180.0
0.0000 0.7072 -0.7070
2 3 90.0 90.0 270.0 51.5 90.0 180.0 90.0
-1.0000 0.0000 0.0000
2 4 90.0 90.0 90.0 51.5 135.0 270.0 180.0
0.0000 -0.7070 -0.7072
3 1 270.0 90.0 270.0 51.5 135.0 90.0 180.0
0.0000 0.7070 -0.7072
3 2 270.0 90.0 90.0 51.5 90.0 360.0 90.0
1.0000 0.0000 0.0000
3 3 90.0 90.0 90.0 51.5 45.0 90.0 180.0
0.0000 0.7072 0.7070
3 4 90.0 90.0 270.0 51.5 90.0 180.0 90.0
-1.0000 0.0000 0.0000
4 1 90.0 90.0 270.0 51.5 90.0 180.0 90.0
-1.0000 0.0000 0.0000
4 2 90.0 90.0 90.0 51.5 135.0 270.0 180.0
0.0000 -0.7070 -0.7072
4 3 270.0 90.0 90.0 51.5 90.0 360.0 90.0
1.0000 0.0000 0.0000
4 4 270.0 90.0 270.0 51.5 45.0 270.0 180.0
0.0000 -0.7072 0.7070
Peak 10
1 1 270.0 90.0 270.0 51.5 45.0 270.0 180.0
0.0000 -0.7072 0.7070
1 2 270.0 90.0 90.0 51.5 90.0 360.0 90.0
1.0000 0.0000 0.0000
1 3 90.0 90.0 90.0 51.5 135.0 270.0 180.0
0.0000 -0.7070 -0.7072
1 4 90.0 90.0 270.0 51.5 90.0 180.0 90.0
-1.0000 0.0000 0.0000
2 1 90.0 90.0 270.0 51.5 90.0 180.0 90.0
-1.0000 0.0000 0.0000
2 2 90.0 90.0 90.0 51.5 45.0 90.0 180.0
0.0000 0.7072 0.7070
2 3 270.0 90.0 90.0 51.5 90.0 360.0 90.0
1.0000 0.0000 0.0000
2 4 270.0 90.0 270.0 51.5 45.0 270.0 180.0
0.0000 -0.7070 0.7072
3 1 90.0 90.0 90.0 51.5 135.0 270.0 180.0
0.0000 -0.7070 -0.7072
3 2 90.0 90.0 270.0 51.5 90.0 180.0 90.0
-1.0000 0.0000 0.0000
3 3 270.0 90.0 270.0 51.5 135.0 90.0 180.0
0.0000 0.7072 -0.7070
3 4 270.0 90.0 90.0 51.5 90.0 360.0 90.0
1.0000 0.0000 0.0000
4 1 270.0 90.0 90.0 51.5 90.0 360.0 90.0
1.0000 0.0000 0.0000
4 2 270.0 90.0 270.0 51.5 135.0 90.0 180.0
0.0000 0.7070 -0.7072
4 3 90.0 90.0 270.0 51.5 90.0 180.0 90.0
-1.0000 0.0000 0.0000
4 4 90.0 90.0 90.0 51.5 45.0 90.0 180.0
0.0000 0.7072 0.7070
Any suggestions and advice are very welcome.
Cheers
James
Dr James Garnett
Centre for Structural Biology
Division of Molecular Biosciences
Level 5 Sir Ernst Chain Building
South Kensington Campus
Imperial College London
London SW7 2AZ
Tel: +44 (0) 207 594 5464
Fax: +44 (0) 207 594 3057
