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: CCP4BB@JISCMAIL.AC.UK
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"
> <[EMAIL PROTECTED]>
> To: <CCP4BB@JISCMAIL.AC.UK>
> 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===========
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Northwestern University
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(847)467-4049
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