Dear Remy,
Indeed, I think you may be correct and we're pursuing this now. A perfect
0.5 lattice translocation along b in P212121 would (I think) result in the
pathology we observe. We do not see zones of streaked reflections in the
images, but my thinking is that if the lattice defect is coincident with a
crystallographic translation operator, perhaps we wouldn't expect to.
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
[log in to unmask]
On 9/3/15 12:49 PM, "Remy Loris" <[log in to unmask]> wrote:
>Dear Mark,
>
>My suspicion is that what you observe here is a lattice disorder,
>possibly related to what is described in
>
>Jimin Wang, Satwik Kamtekar, Andrea J. Berman and Thomas A. Steitz
>(2005) Correction of X-ray intensities from single crystals containing
>lattice-translocation defects Acta Cryst D61, 67-74.
>
>If your unit cell is offset statistically by 0.5 in the b-direction,
>this should provide such a strong non-origin peak as you observe. In the
>cases that have been described until now, this type of disorder also
>involves zones of nice sharp reflections and other zones with more
>streaky reflections. Do you see something similar?
>In order to use such data, they have to be corrected as described in the
>paper above.
>
>Possibly, the crystals with the 10% non-origin peak also have the
>disorder, but much less pronounced so that omitting the required
>correction did not prevent structure determination and refinement
>(similar to let say a small fraction of merohedral twinning that is
>overlooked).
>
>Remy Loris
>Vrije Universiteit Brussel and VIB
>
>DOI: 10.1107/S0907444904026721
>
>On 03/09/15 18:13, George Sheldrick wrote:
>> Dear Mark,
>>
>> Since your resolution is good enough, perhaps you should try to solve
>> it ab initio with Arcimboldo Lite. This has already solved a number of
>> structures that turned out to be unexpected.
>>
>> Best wishes, George
>>
>>
>> On 09/03/2015 05:44 PM, Mark Wilson wrote:
>>> Hi Herman,
>>> A fair point-the odds of "depressing coincidence" do seem to be
>>> climbing!
>>> We did inspect the deposited data for a similar peak and, while one is
>>> present, it is only ~10% of the origin and at a different location.
>>> We'll
>>> do some due diligence on our end by re-dissolving crystals and
>>> performing
>>> mass spec. As there seems to be some interest in this, I'll update
>>>once
>>> we've figured it out, even if it's an embarrassing case of wrong
>>> protein,
>>> same cell.
>>> 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
>>> [log in to unmask]
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 9/3/15 10:25 AM, "CCP4 bulletin board on behalf of
>>> [log in to unmask]"<[log in to unmask] on behalf of
>>> [log in to unmask]> wrote:
>>>
>>>> Dear Mark,
>>>>
>>>> In this case you will have to apply Baysian statistics: given the
>>>> prior:
>>>> same protein, same space group same cell dimensions and molecular
>>>> replacement fails completely, the likelihood of having some depressing
>>>> coincidence somewhere is approaches 100%!
>>>>
>>>> What I would do in addition to excellent suggestions you already
>>>> got, is
>>>> to try to download the Fobs from the pdb for the structures with the
>>>> same
>>>> protein, space group and cell dimensions, and calculate pattersons
>>>>with
>>>> those. Sometimes strong peaks appear in pattersons for no obvious
>>>> reasons.
>>>> I would also consider statistical disorder, which will not show up in
>>>> twinning statistics since in this case F's (including phases) are
>>>>added
>>>> instead of I's. Anyways, it will be an interesting puzzle to solve!
>>>>
>>>> Good luck,
>>>> Herman
>>>>
>>>>
>>>> -----Ursprüngliche Nachricht-----
>>>> Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von
>>>> Mark Wilson
>>>> Gesendet: Donnerstag, 3. September 2015 02:06
>>>> An: [log in to unmask]
>>>> Betreff: Re: [ccp4bb] Translational NCS with one molecule in ASU
>>>>
>>>> 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
>>>> [log in to unmask]
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 9/2/15 5:30 PM, "CCP4 bulletin board on behalf of Eleanor Dodson"
>>>> <[log in to unmask] on behalf of [log in to unmask]> 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
>>>>> <[log in to unmask]> 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<[log in to unmask]>
>>>>>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> [log in to unmask]
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>
>>
>
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