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How similar is this data set to the previously crystallised one? 
I think you said there is no translation vector in the previous one so they can't be very similar.
Maybe it is time for experimental phases! 
Eleanor

  

On 3 September 2015 at 21:47, Adrian Goldman <[log in to unmask]> wrote:
This would be my feeling too - one real 21, a twin axis and pseudosymmetry. The standard perfect storm.

Sent from my iPhone

> On 3 Sep 2015, at 21:07, Mark Wilson <[log in to unmask]> wrote:
>
> Hi Eleanor,
> Yes, of course you are correct about the beta~90° requirement for possible
> twinning here-I was mistakenly thinking about pseudomerohedry in higher
> symmetry space groups. The L plot looks like well-behaved data, with a
> straight line that closely tracks the model untwinned one.  Pointless,
> provided with data integrated in P1, choses P212121 with high  confidence
> (0.95-0-.99), which is similar to the results of analysis using xtriage in
> PHENIX.  Unsymmetrized cell angles are within 0.02-0.05° of 90°.  Finally,
> the protein we crystallized is (to-be-tested wrong protein scenario aside)
> identical to the previously crystallized one, and our unit cell axes are
> the same within 5% or so.
> 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 2:45 PM, "Eleanor Dodson" <[log in to unmask]> wrote:
>>
>> Disorder almost always produces streaked spots, but I guess it isn't
>> compulsory!
>>
>> By the way, you can have twinning in Monoclinic if B ~ 90. without having
>> a = c.
>>
>>
>> . What does the L plot look like? Have you used pointless which gives the
>> CC for each symmetry operator separately - sometimes that shows say the
>> 00 l axis is more 2-fold ish than the 0k0 axis..
>>
>>
>>
>> Eleanor
>> PS - If the related protein fits into a similar cell with the same SG is
>> yours bigger?
>>
>>
>>
>>
>> On 3 September 2015 at 18:56, Mark Wilson
>> <[log in to unmask]> wrote:
>>
>> 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 <tel:%28402%29%20472-3626>
>> [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 <tel:%28402%29%20472-3626>
>>>>>> [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>
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