Dear Garib,
I have run the jellybody refinement and whilst it has not reduced the Rfactors
I am going to see whether I can see anything usable in the new maps.
many thanks
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
________________________________
From: Garib N Murshudov [ga...@mrc-lmb.cam.ac.uk]
Sent: 09 July 2012 12:07
To: Garnett, James A
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Rfactors stuck very high
Dear James
It seems that at this stage you may not be able to distinguish between these
space groups. As I see they are subgroup of each other (more precisely P1 < C2
< I222 with the cell parameters you have) and it would not be easy to find out
the exact space group at this stage. Highest space group may be more likely
than others in the absence of other evidences.
It seems that the problem is that the model is sufficiently far and refinement
programs struggle to converge. We had some good results for this type of cases
when we used jelly body refinement in refmac with 40-100 cycles and sigma set
to 0.01. Phenix may have similar tricks.
After that you can try either shelxe or arpwarp or one after another. Although
at 2.3A they may not produce results as spectacular as in presentations, they
may give you improved maps to work with.
regards
Garib
On 8 Jul 2012, at 22:11, James Garnett wrote:
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
Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk<mailto:jen...@mrc-lmb.cam.ac.uk>
Web http://www.mrc-lmb.cam.ac.uk<http://www.mrc-lmb.cam.ac.uk/>
