Hi All,
An important point is that the cell dimensions are: 54.98 58.45 66.89 90
90 90. While a and b are similar, they are (in my opinion) not similar
enough to support pseudo-merohedral twinning. The absences are indeed
absent, with I/sigma(I) between ~ -1 and 2. All three axes have similarly
convincing absences in P212121, included below.
Best regards,
Mark
==============
Intensities of systematic absences
h k l Intensity Sigma I/Sigma
0 0 5 1.8 2.5 0.7
0 0 7 -4.1 3.5 -1.2
0 0 9 9.9 4.6 2.2
0 0 11 -1.1 6.5 -0.2
0 0 13 12.9 10.0 1.3
0 0 15 -7.2 9.9 -0.7
0 0 17 -11.2 8.8 -1.3
0 0 19 1.1 10.0 0.1
0 0 21 -1.4 9.3 -0.2
0 0 23 0.8 9.3 0.1
0 0 25 1.5 8.1 0.2
0 0 27 7.4 9.3 0.8
0 3 0 -1.6 4.5 -0.4
0 5 0 -4.7 5.5 -0.9
0 7 0 -18.1 12.2 -1.5
0 9 0 13.0 13.6 1.0
0 11 0 19.3 18.6 1.0
0 13 0 51.6 29.8 1.7
0 15 0 38.6 24.4 1.6
0 17 0 -9.5 30.2 -0.3
0 19 0 -42.8 36.1 -1.2
0 21 0 -12.5 22.4 -0.6
0 23 0 -3.2 24.9 -0.1
0 25 0 54.8 38.7 1.4
0 27 0 -28.2 36.2 -0.8
0 29 0 -0.1 30.6 0.0
0 31 0 -25.7 39.8 -0.6
0 33 0 -11.6 38.1 -0.3
3 0 0 1.6 3.3 0.5
5 0 0 9.2 5.2 1.8
7 0 0 -0.4 9.6 0.0
9 0 0 -2.7 11.2 -0.2
11 0 0 65.1 21.1 3.1
13 0 0 19.8 19.0 1.0
15 0 0 -24.5 20.9 -1.2
17 0 0 29.9 31.8 0.9
19 0 0 -3.3 24.3 -0.1
21 0 0 -33.4 33.0 -1.0
23 0 0 -4.8 29.4 -0.2
25 0 0 -6.7 33.3 -0.2
27 0 0 55.3 37.6 1.5
29 0 0 11.0 38.6 0.3
31 0 0 -36.4 46.6 -0.8
Mark A. Wilson
Associate Professor
Department of Biochemistry/Redox Biology Center
University of Nebraska
N118 Beadle Center
1901 Vine Street
Lincoln, NE 68588
(402) 472-3626
[email protected]
On 9/3/15 1:51 AM, "CCP4 bulletin board on behalf of Adrian Goldman"
<[email protected] on behalf of [email protected]> wrote:
>I agree. This was essentially Eleanor's viewpoint too. So p21
>merohedrally twinned to orthorhombic with the 0.47 translational ncs.. I
>would look at the h00, k00, l00 odd peaks (the ones systematically
>disallowed) to look for evidence of some intensity
> along one of the axes in the disallowed spots. That will help establish
>which axis has the true 21 screw. My guess is that at high Bragg angle
>there is some intensity in the k odd spots at least.
>
>
>Adrian
>
>Sent from my iPad
>
>On 3 Sep 2015, at 6:40 am, Sudipta Bhattacharyya
><[email protected]> wrote:
>
>
>
>Hi Mark,
>
>
>One strategy that worked for me is to reprocess/expand the data to P1 and
>try to do MR in that SG, do initial one cycle of rigid body and
>restrained refinements and then you can feed the P1 data and the model to
>zanuda to get correct assessment of SG.
> Then you have to reprocess the data accordingly. Anyway, twining tests
>are most of the time obscured when tNCS is present. So, I think, the
>presence of twining can't be simply overruled in this case. reprocessing
>the data in monoclinic SG, followed by doing
> MR could be the key to this problem.
>
>
>Good luck..!!!
>Sudipta
>
>
>On Wed, Sep 2, 2015 at 6:05 PM, Mark Wilson
><[email protected]> wrote:
>
>Dear CCP4 Community,
>I've had a number of helpful responses (on- and off-list) that I will
>briefly summarize via response, including information that I probably
>should have included in the original post. Many have suggested a wrong
>space group, which I agree seems probable. MR was attempted in PHASER
>with all possible choices of space group for a primitive orthorhombic
>lattice, and in all cases failed with no rotation or translation peaks
>above a Z-score of 5.
> I've not yet tried monoclinic lattices and will, but this still
>wouldn't
>explain (to me anyway) an apparently impossible combination of
>translational NCS in P212121 with a cell that can't accommodate a second
>molecule unless twinning was also present, which may be the case (as
>Eleanor suggested). Others have asked about evidence of missed weak
>reflections indicating a larger true cell, which I looked for but didn't
>see in these images. The crystal that was used was mounted at room
>temperature, so there is no opportunity for cryo artifacts to have done
>something strange to the cell.
> Other suggestions included the presence of strong internal
>symmetry in
>the molecule, which is present, but as a pseudo-threefold, which seems
>incompatible with my NCS centering operation. One respondent suggested
>that we've crystallized the wrong molecule, which is something I also
>worried about a bit. Although possible, the space group and cell for our
>crystal are both as previously reported for this protein by another group,
>so it would be a depressing coincidence if we crystallized the wrong
>protein in the same cell. I'll be happy to update if/when we figure this
>out should it be of interest to the board. Thank you all for your
>thoughtful responses, which arrived in impressive number in the time it
>took me to drive home.
>Best regards,
>Mark
>
>Mark A. Wilson
>Associate Professor
>Department of Biochemistry/Redox Biology Center
>University of Nebraska
>N118 Beadle Center
>1901 Vine Street
>Lincoln, NE 68588
>(402) 472-3626 <tel:%28402%29%20472-3626>
>[email protected]
>
>
>
>
>
>On 9/2/15 5:30 PM, "CCP4 bulletin board on behalf of Eleanor Dodson"
><[email protected] on behalf of
>[email protected]> wrote:
>
>>Well - a translation of 0 0.5 0 would generate absences along b so that
>>the SG could be P212121 or P 21 2 21Š
>>
>>
>>I would suspect twinning and a monoclinic SG .
>>Or as we found sadly - half the protein had disappeared in the
>>crystallisation trials..
>>
>>
>>But such a translation must mean you almost have a halved unit cell?
>>Another way of saying there isn't enough room for your molecule..
>>
>>
>>
>>On 2 September 2015 at 22:38, Shane Caldwell
>><[email protected]> wrote:
>>
>>Are you certain it's actually P212121? One possibility is you're at lower
>>symmetry and the Patterson peak corresponds to the NCS between particles
>>that are almost-but-not-quite crystallographically equivalent. In that
>>case, MR probably wouldn't
>> work. Does searching in P1 find anything?
>>
>>Shane Caldwell
>>
>>McGill University
>>
>>
>>
>>
>>
>>On Wed, Sep 2, 2015 at 5:19 PM, Mark Wilson
>><[email protected]> wrote:
>>
>>Dear CCP4 community,
>>I've encountered a curious problem with some recently collected data. I
>>have a 1.8 Å resolution dataset that scales well in P212121 (log file
>>available upon request). The unit cell parameters are similar to those
>>reported for crystals of the same protein in a previous publication,
>>although my crystallization condition is different. Nevertheless, my
>>data
>>produce a strong (47% of origin) peak in the Patterson map at 0.0, 0.5,
>>0.0, indicative of translational NCS. However, the unit cell parameters
>>can accommodate only one molecule in the ASU without single-digit solvent
>>content. Moreover, molecular replacement with a model that should be
>>nearly identical fails. Standard intensity-based tests show no evidence
>>of twinning or other data pathology. Any thoughts would be appreciated.
>>Best regards,
>>Mark
>>
>>Mark A. Wilson
>>Associate Professor
>>Department of Biochemistry/Redox Biology Center
>>University of Nebraska
>>N118 Beadle Center
>>1901 Vine Street
>>Lincoln, NE 68588
>
>
>>(402) 472-3626 <tel:%28402%29%20472-3626> <tel:%28402%29%20472-3626>
>>[email protected]
>>
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