Beware twinning tests with pseudo translation! Intensity stats are
distorted..
What does SFCHECK suggest? It pre-selects data for testing..
Eeanor
Green, Todd wrote:
>
> I have a case that is similar to this, or at least visually similar by
> diffraction pattern(ie. strong/weak intensities). I think my situation
> is due to a pseudo-translation. I say this my defining of pseudo
> translation as basically something other than pure translation(ie.
> some translation and some degree (albeit slight) of rotation). In my
> case, the crystals (I THINK!) are P23(and i guess you would say pseudo
> I23). There are assemblies at 0,0,0 and 0.5,0.5,0.5. The "translated"
> assembly at 0.5,0.5,0.5 is slightly misaligned(by a small rotation)
> with the assembly at the origin but near to perfect. If it were
> perfect it'd be I23. But since it is not, it is reduced to the
> Primitive cell. When indexing, if you don't include the more diffuse,
> lower intensity spots, you will lock on the I-cell. If you include
> them then you get right cell, as you would suspect. I included
> pictures. These are 2 regions of a single diffraction pattern with
> spot predictions for the indicated Bravais lattice. You can easily
> see the sharper more dense spots versus the more diffuse less intense
> ones. In the second shot, you can see that the orthorhombic cell fits
> much better than either of the cubic cells but that's another issue
> which is related to my questions last week. So to muddy the water a
> little, my case could be pseudo-cubic altogether. I'm still working on
> all of that. As a side note, Xtriage doesn't think things are twinned
> as was suggested for one some of the other diffraction patterns
> discussed earlier today.
>
> -Todd
>
>
>
>
> -----Original Message-----
> From: CCP4 bulletin board on behalf of Jacob Keller
> Sent: Mon 8/27/2007 10:44 AM
> To: [log in to unmask]
> Subject: [ccp4bb] Strange diffraction images
>
> What a beautiful and interesting diffraction pattern!
>
> To me, it seems that there is a blurred set of spots with different
> cell dimensions, although
> nearly the same, underlying the ordered diffraction pattern. A
> possible interpretation occurred to
> me, that the ordered part of the crystal is supported by a
> less-ordered lattice of slightly
> different dimensions, which, because the crystal is a like a
> layer-cake of 2-d crystals, need not
> be commensurable in the short range with the ordered lattice. The
> nicely-ordered "cake" part of the
> crystal you solved, but the "frosting" between is of a different, less
> ordered nature, giving rise
> to the diffuse pattern which has slightly different lattice spacing. I
> would have to see more
> images to know whether this apparent lattice-spacing phenomenon is
> consistent, but it at least
> seems that way to me from the images you put on the web. I would
> shudder to think of indexing it,
> however.
>
> All the best,
>
> Jacob Keller
>
> ps I wonder whether a crystal was ever solved which had two
> interpenetrating, non-commensurable
> lattices in it. That would be pretty fantastic.
>
> ==============Original message text===============
> On Mon, 27 Aug 2007 5:57:45 am CDT "Mark J. van Raaij" wrote:
>
> In general, I think we should be careful about too strong statements,
> while in general structures with high solvent diffract to low-res,
> there are a few examples where they diffract to high res. Obviously,
> high solvent content means fewer crystal contacts, but if these few
> are very stable?
> Similarly, there are probably a few structures with a high percentage
> of Ramachandran outliers which are real and similarly for all other
> structural quality indicators. However, combinations of various of
> these probably do not exist and in any case, every unusual feature
> like this should be described and an attempt made to explain/analyse
> it, which in the case of the Nature paper that started this thread
> was apparently not done, apart from the rebuttal later (and perhaps
> in unpublished replies to the referees?).
>
> With regards to our structures 1H6W (1.9A) and 1OCY (1.5A), rather
> than faith, I think the structure is held together by a real
> mechanism, which however I can't explain. Like in the structure Axel
> Brunger mentioned, there is appreciable diffuse scatter, which imo
> deserves to be analysed by someone expert in the matter (to whom, or
> anyone else, I would gladly supply the images which I should still
> have on a tape or CD in the cupboard...). For low-res version of one
> image see
> http://web.usc.es/~vanraaij/diff45kd.pngand
> <http://web.usc.es/%7Evanraaij/diff45kd.pngand>
> http://web.usc.es/~vanraaij/diff45kdzoom.pngtwo
> <http://web.usc.es/%7Evanraaij/diff45kdzoom.pngtwo> possibilities I
> have been thinking about:
> 1. only a few of the "tails" are ordered, rather like a stack of
> identical tables in which four legs hold the table surfaces stably
> together, but the few ordered tails/legs do not contribute much to
> the diffraction. This raises the question why some tails should be
> "stiff" and others not; perhaps traces of a metal or other small
> molecule stabilise some tails (although crystal optimisation trials
> did not show up such a molecule)?
> 2. three-fold disorder, either individually or in microdomains too
> small to have been resolved by the beam used. For this I have been
> told to expect better density than observed, but maybe this is not true.
> we did try integrating in lower space groups P3, P2 instead of P321
> with no improvement of the density, we tried a RT dataset to see if
> freezing caused the disorder and we tried improving the phases by MAD
> on the mercury derivative, but with no improvement in the density for
> the tail.
>
> Mark J. van Raaij
> Unidad de Bioquímica Estructural
> Dpto de Bioquímica, Facultad de Farmacia
> and
> Unidad de Rayos X, Edificio CACTUS
> Universidad de Santiago
> 15782 Santiago de Compostela
> Spain
> http://web.usc.es/~vanraaij/ <http://web.usc.es/%7Evanraaij/>
>
> On 24 Aug 2007, at 03:01, Petr Leiman wrote:
>
> > ----- Original Message ----- From: "Jenny Martin"
> > <[log in to unmask]>
> > To: <[log in to unmask]>
> > Sent: Thursday, August 23, 2007 5:46 PM
> > Subject: Re: [ccp4bb] The importance of USING our validation tools
> >
> >> My question is, how could crystals with 80% or more solvent
> >> diffract so well? The best of the three is 1.9A resolution with I/
> >> sigI 48 (top shell 2.5). My experience is that such crystals
> >> diffract very weakly.
> >
> > You must be thinking about Mark van Raaij's T4 short tail fibre
> > structures. Yes, the disorder in those crystals is extreme. There
> > are ~100-150 A thick disordered layers between the ~200 A thick
> > layers of ordered structure. The diffraction pattern does not show
> > any anomalies (as far as I can remember from 6 years ago). The
> > spots are round, there are virtually no spots not covered by
> > predictions, and the crystals diffract to 1.5A resolution. The
> > disordered layers are perpendicular to the threefold axis of the
> > crystal. The molecule is a trimer and sits on the threefold axis.
> > It appears that the ordered layers somehow know how to position
> > themselves across the disordered layers. I agree here with Michael
> > Rossmann that in these crystals the ordered layers are held
> > together by faith.
> > Mark integrated the dataset in lower space groups, but the
> > disordered stuff was not visible anyway. He will probably add more
> > to the discussion.
> >
> > Petr
> >
> >
> >>
> >> Any thoughts?
> >>
> >> Cheers,
> >> Jenny
>
> ===========End of original message text===========
>
>
>
> ***********************************
> Jacob Keller
> Northwestern University
> 6541 N. Francisco #3
> Chicago IL 60645
> (847)467-4049
> [log in to unmask]
> ***********************************
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