Hi,
In the presence of tNCS, the normal moments tests can indeed be difficult to interpret: twinning makes the 2nd moments smaller, whereas tNCS makes them bigger. However, you can use Phaser to compensate for this effect, by characterising the tNCS and accounting for its statistical effect on the distribution of intensities. In the case of 2-fold tNCS, this usually works pretty well and both the cumulative distributions and the 2nd moments can then reveal the presence of twinning. This would be worth trying, and it works better than trying to test the distributions for a supercell. Note that you want to provide the data in terms of intensities, not amplitudes, for this to work best.
The L-test should be reasonably unaffected by twinning and does, in this case, seem to suggest at least partial twinning.
If you have a really good model, I would suggest trying molecular replacement in P1 first, because if you get a clear solution the symmetry of the solution will tell you what the true space group is.
Best wishes,
Randy Read
-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills Road E-mail: [log in to unmask]
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
> On 3 Dec 2017, at 19:52, Eleanor Dodson <[log in to unmask]> wrote:
>
> Certainly you may have a lower symmetry spacegroup, but with NC translation the twinning tests are a bit uncertain.
>
> Your moments seem too high, whereas twinning usually makes them too low. But we need to see the plots v resolutio which should be pretty linear..
> Sometimes these go haywire at higher resolution..
>
>
> And also the spacegroup determination - absences along a* and C*could be caused by the translation (1/2,0.4,1/2) so you need to test P2 21 2 and P 21 21 2 and P 2 21 21 etc..
>
> This is messy but you can test the data h'=h/2 k l'=l/2 ( Ie for a cell 2a,b,2c and see if that seems twinned
>
> (Use reindex and requset
> h/2,k,l/2 as the reindexing operator then input it to ctruncate ..)
>
>
>
> And of course if th integration is a bit ropy you can get strange effects.. Do you see the same results for all crystals?
>
> Eleanor
>
> On 3 December 2017 at 18:42, Kay Diederichs <[log in to unmask]> wrote:
> Hi Carmela,
>
> as Jacob suggests, the real space group may be P2 or P2(1). You need to prepare 3 MTZ files, each corresponding to a different unique b axis.
> So just run XDS 3 times, each time with JOB=CORRECT and SPACE_GROUP_NUMBER=3, and afterwards XDSCONV to create a MTZ file (or pointless/aimless).
>
> First time:
> UNIT_CELL_CONSTANTS= 58 103 220 90 90 90
> Second time:
> UNIT_CELL_CONSTANTS= 103 220 58 90 90 90
> Third time:
> UNIT_CELL_CONSTANTS=220 58 103 90 90 90
>
> Then, if you have a good model, do MR with each MTZ file, taking care that both P2 and P2(1) are tested. Or experimental phasing, but that requires good data.
>
> HTH,
> Kay
>
> On Sun, 3 Dec 2017 18:29:57 +0100, Carmela Garcia <[log in to unmask]> wrote:
>
> >Hi,
> >
> >The dimensions for a native are 58 103 220, with small differences for the derivatives.
> >
> >Best,
> >
> >Carmela.
> >
> >> On 3 Dec 2017, at 18:18, Sridhar Prasad <[log in to unmask]> wrote:
> >>
> >> Hello,
> >> Can you please share the unit cell dimensions.
> >>
> >> Cheers,
> >> Sridhar
> >>
> >> On Dec 3, 2017 9:13 AM, "Carmela Garcia" <[log in to unmask] <mailto:[log in to unmask]>> wrote:
> >> Dear all,
> >>
> >> I know that some years ago a similar situation was discussed here, and I wonder if someone has new insights about these problems.
> >>
> >> My protein is a dimer in solution. I tried several derivatives for SAD, and all my datasets seem to have the same problem, including the native crystals. I processed the data with XDS and the space group determination was done with Pointless, being a P212121.
> >>
> >> Checking the quality of the data, I found several problematic results:
> >>
> >> - Translational NCS is detected. There is a peak at (0.50, 0.40, 0.50)
> >> - The L test suggests twinning (L statistic = 0.41)
> >> - The mean acentric moments I from input data have the following values:
> >> <I^2>/<I>^2 : 4.396
> >> <I^3>/<I>^3: 34.478
> >> <I^4>/<I>^4: 361.084
> >> All these values are way higher than the expected ones for non-twinned data.
> >> - The twinning fraction from L-test is 0.22
> >>
> >> This would all suggest that my space group is wrong, and that I should proceed in a lower symmetry group, but I don’t know how should I continue. I know about cases where a P43212 or a P41212 were suggested but in fact the correct space group was P212121, but I would not know how to continue going down. Checking my images, I can see some streaky spots, and the crystals grow first as needles that eventually become plates and rarely crystals. All these would be a clear indicative of twinning, but I would not expect to have the same results with different derivatives. We thought about some kind of reticular twinning, and I wonder if there is a way to solve it.
> >>
> >> Any idea about how to proceed or to identify the problem would be welcome.
> >>
> >> Thanks,
> >>
> >> Carmela.
> >>
> >>
> >>
> >> Carmela Garcia-Doval
> >> University of Zurich
> >> Department of Biochemistry
> >> Winterthurerstrasse 190 <https://maps.google.com/?q=Winterthurerstrasse+190&entry=gmail&source=g>
> >> CH-8057 Zurich
> >> Switzerland
> >> E-mail: [log in to unmask] <mailto:[log in to unmask]>
> >
> >
>
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