Re: [ccp4bb] AW: [ccp4bb] Translational NCS with one molecule in ASU

[Mark Wilson]

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
mwilso...@unl.edu 






On 9/3/15 10:25 AM, "CCP4 bulletin board on behalf of
herman.schreu...@sanofi.com"  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:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
>Mark Wilson
>Gesendet: Donnerstag, 3. September 2015 02:06
>An: CCP4BB@JISCMAIL.AC.UK
>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
>mwilso...@unl.edu 
>
>
>
>
>
>On 9/2/15 5:30 PM, "CCP4 bulletin board on behalf of Eleanor Dodson"
> 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
>> 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 

Re: [ccp4bb] AW: [ccp4bb] Translational NCS with one molecule in ASU

[Mark Wilson]

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
mwilso...@unl.edu 






On 9/3/15 12:49 PM, "Remy Loris"  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
>>> mwilso...@unl.edu
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 9/3/15 10:25 AM, "CCP4 bulletin board on behalf of
>>> herman.schreu...@sanofi.com">> herman.schreu...@sanofi.com>  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:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
 Mark Wilson
 Gesendet: Donnerstag, 3. September 2015 02:06
 An: CCP4BB@JISCMAIL.AC.UK
 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 

Re: [ccp4bb] AW: [ccp4bb] Translational NCS with one molecule in ASU

[Mark Wilson]

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
mwilso...@unl.edu 






On 9/3/15 2:45 PM, "Eleanor Dodson"  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
> 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 
>mwilso...@unl.edu
>
>
>
>
>
>
>On 9/3/15 12:49 PM, "Remy Loris"  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
 mwilso...@unl.edu






 On 9/3/15 10:25 AM, "CCP4 bulletin board on behalf of
 herman.schreu...@sanofi.com"  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

Re: [ccp4bb] AW: [ccp4bb] Translational NCS with one molecule in ASU

[Mark Wilson]

Hi Eleanor,
I agree that experimental phases may be needed, although I may take the
lazy way out and just aggressively screen for a less problematic crystal
form.
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
mwilso...@unl.edu 






On 9/3/15 4:06 PM, "CCP4 bulletin board on behalf of Eleanor Dodson"
 wrote:

>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
> 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  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
>> mwilso...@unl.edu
>>
>>
>>
>>
>>
>>
>>> On 9/3/15 2:45 PM, "Eleanor Dodson"  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
>>>  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  
>>> mwilso...@unl.edu
>>>
>>>
>>>
>>>
>>>
>>>
 On 9/3/15 12:49 PM, "Remy Loris"  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