Hi Marcelo,
based on this image it looks like you have multiple (two) lattices, which
puts spots very close together. This could be a split crystal as Eleanor
suggested, or a feature of the way the crystals grow. It seems unlikely that
you’d be able to integrate these lattices well, given how close the spots are.
You could try data collection with the detector pushed further back to increase
spot separation (not an ideal solution). If the multiple lattices is something
you see with all crystals then you may want to work on modifying
crystallization conditions.
Sometimes things can be very difficult to figure out. The Dicer structure
(see Ian MacRae’s paper in Acta D: D63, 993-999, 2007) was a case where the a
and b axes of the orthorhombic lattice were very similar in length and the
crystals always grew with a pseudo-merohedral twinning that gave rise to
nearly, but not quite, overlapped spots from the two lattices. It doesn’t look
like you have a case like this, because the intensity statistics don’t suggest
twinning. However, some of the tricks that you might use today on such
crystals, such as raster scanning with a microbeam, might be helpful.
Cheers,
Paul
> On Aug 12, 2018, at 9:57 AM, Randy Read <rj...@cam.ac.uk> wrote:
>
> I am sorry. I forgot to attach the image.
>
> Cheers
>
> Marcelo
>
> Em sáb, 11 de ago de 2018 às 18:31, Marcelo Liberato
> <marcelovliber...@gmail.com> escreveu:
> Dear Eleanor,
>
> Thanks for you answer.
> Indeed, there are clear ice rings in the images (example attached). So, I
> integrated again (P1, P2 and P222) excluding the resolution ranges 2.28-2.22
> and 3.70-3.64. I am attaching the log files from aimless, MR and refmac for
> P2 (in two different cells) and P222 data.
> I agree that MR seems very good (in all cases), but the final density maps
> are always bad. Maybe the data has problems that I am not dealing with.
>
> Kind regards
>
> Marcelo
>
> Em sáb, 11 de ago de 2018 às 16:04, Eleanor Dodson
> <eleanor.dod...@york.ac.uk> escreveu:
> This MR looks good to me, but there are serious flaws with the data. Your
> secon moment plot from the aimless log has most spectacular spikes which are
> always a BAD THING, and the Wilson plot is not very smooth either..
>
> As Randy says, try to sort those problems out first.
>
> Then you have this message:
>
>
> TRANSLATIONAL NCS:
>
> Translational NCS has been detected at ( 0.000, 0.500, 0.125).
> A translation of 0.5 along B will generate pseudo-absences along b so you can
> be sure whether there is a scre axis or not..
>
> The space group is most likely orthorhombic - these indicators are pretty
> convincing for P2/mmm - so I dont know why you have chosen P21 as the
> spacegroup?
>
>
> Scores for each symmetry element
>
> Nelmt Lklhd Z-cc CC N Rmeas Symmetry & operator (in Lattice
> Cell)
>
> 1 0.917 8.18 0.82 61009 0.298 identity
> 2 0.883 7.85 0.78 100711 0.381 ** 2-fold l ( 0 0 1) {-h,-k,l},
> along original k
> 3 0.921 8.39 0.84 99542 0.355 *** 2-fold k ( 0 1 0) {-h,k,-l},
> along original l
> 4 0.920 8.26 0.83 99218 0.320 *** 2-fold h ( 1 0 0) {h,-k,-l},
> along original h
>
> So my suggestions:
> Sort out data problems
>
> Merge as P2/mmm
>
> Let MR search select the most likely spacegroup of the 8 possible.
>
> You cant even limit the b axis to be a screw axis .
>
> Your refinement behavior looks OK, but the maps will look bad with spurious
> reflections in the list..
>
> Eleanor
>
>
>
>
>
> On 10 August 2018 at 19:02, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote:
> Actually Marcelo - Refinement to an R of 41% is pretty good for an MR
> solution!
>
>
>
> On 10 August 2018 at 18:42, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote:
> Can you attach the refinement log?
>
> Eleanor
>
> On 10 August 2018 at 16:57, Marcelo Liberato <marcelovliber...@gmail.com>
> wrote:
> Dear Randy,
>
> Thank you very much for answering. I followed your suggestions but,
> unfortunately, I couldn't get a reasonable electron density map after MR and
> refinement.
>
>
> First I would look at the data to see if you have ice rings, because the peak
> in mean intensity and second moment of the intensity at about 2.25A
> resolution suggests an ice ring problem. If so, you should make sure you
> don't contaminate the data with spurious large intensities.
>
> Indeed, the data has ice rings. At first, I required imosflm to remove ice
> rings, but it didn't happened. So, I re-processed the data in different space
> groups removing the ice rings.
>
> Second, the statistics (e.g. the second moments plot after tNCS correction in
> Phaser) would be consistent with a scenario in which you have pseudosymmetry
> along with a twin operator that parallels the pseudosymmetry. If that's
> true, it's hard to be sure of the symmetry. For instance, if the structure
> really is monoclinic, can you be sure you chose the correct axis to be the
> 2-fold?
>
> I am not sure. However, I tried two possible axis to be the 2-fold and none
> of them gave me reasonable maps after MR and refinement.
>
>
> Since you have a good model that gives clear MR solutions even in P21, you
> can probably process the data in P1 and solve it with 8 copies in the unit
> cell. Then you can look at the symmetry of the MR solution (e.g. in Zanuda)
> and see whether it obeys any higher symmetry than P1.
>
> I processed data in P1. After MR (with 8 copies in the ASU), it resulted in
> TFZ=11.6 and LLG=1434. But the map is still bad and high Rwork and Rfree.
> According to Zanuda, the data should be P21:
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> | >> 4 | P 1 21 1 | 68.6868 | 0.6289 | 0.5487 | 0.5523 |
> ---------------------------------------------------------------------
> | 1 | P 1 | 69.4151 | 0.6171 | 0.5471 | 0.5559 |
> | 4 | P 1 21 1 | 69.3810 | -- | 0.5482 | 0.5442 |
> | 11 | P 21 21 21 | 52.0271 | -- | 0.6107 | 0.6178 |
> ---------------------------------------------------------------------
> | << 4 | P 1 21 1 | 69.3810 | -- | 0.5482 | 0.5442 |
> ---------------------------------------------------------------------
> I processed in P21 using two different unit cells, and MR resulted in
> TFZ=20.8 and LLG=511, and TFZ=56 and LLG=2867. However, again, no good maps
> and statistics.
>
> Best regards
>
> Marcelo Liberato
>
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> <image 1.jpg>
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Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence
Berkeley Lab
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Adjunct Professor, Department of Bioengineering, U.C. Berkeley
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