Re: [ccp4bb] small lines in diffraction pattern

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: small lines in diffraction pattern
From: Robert Sweet rsweet {- at -} BNL {- dot -} GOV
Date: 2009-01-28

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Subject: Re: small lines in diffraction pattern
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Subject: Re: small lines in diffraction pattern
From: Jürgen_Bosch jubosch {- at -} JHSPH {- dot -} EDU
Date: 2009-01-28

Hi James,

what your descriptions aims at is I think shown in this publication
Borgstahl, G. E. O. "Incommensurate Crystallography by Sander van
Smaalen" Crystallography reviews 14 , 259-260 (2008).

Or am I misunderstanding something here ?

Jürgen

On 28 Jan 2009, at 12:39, James Holton wrote:

> I recommend you have a look at a book from OUP called "Diffuse X-Ray
> Scattering and Models of Disorder" by T. R. Welberry. The first
> chapter
> explains quite well (I think) where all these streaky things come
> from.
> It will also make you feel better about having it when you see all the
> small molecule structures that have horrible diffuse scattering! (such
> as urea).
>
> This looks to me like a fairly classic case of correlated static
> disorder. Best way to think about it is this:
>
> Imagine you have two different kinds of unit cells: A an B. Doesn't
> really matter what the difference between A and B is, could be a
> two-headed side chain in conformer A vs conformer B, or it could be as
> complicated as a domain motion. But, for simplicity, lets assume it
> is
> two rotamers of a side chain and also assume that each unit cell in
> your
> crystal can only be one or the other (no "in betweens").
>
> Now, if the arrangement of these unit cells is perfectly correlated
> and
> an "A" always occurs right next door to a "B" along the c-axis (say),
> then what you really have is a bigger unit cell than you think. That
> is, you can draw a unit cell around each A-B pair and call it a
> "supercell" with the contents of B as a simple NCS mate of A (with one
> side chain in a different rotamer). Some people might call this a
> "pseudotranslation". The effect on the diffraction pattern in this
> case
> would be the appearance of a very weak spot in between each "old" spot
> along your "c" axis. That is, your "supercell" is twice as big along
> "c" so the reciprocal-space lattice has twice as many spots in it.
> The
> new spots are weak because they only correspond to the differences
> between A and B, which in this case is only a few atoms.
>
> Now lets say A and B are not perfectly correlated, but only slightly.
> That is, in some parts of the crystal A and B are side-by-side, but in
> other parts you get AAB, ABBA, BABBA, etc. In each of these cases the
> "supercell" you must draw is 3, 4 and 5x your original unit cell.
> Each
> of these will produce new weak spots with progressively tighter
> spacings. As the supercell becomes very long, these rows of tight
> spots
> will become a streak. The streaks are particularly prominent if the
> A-B
> disorder is along only one axis. In that case, you must have a whole
> a-b layer of "A" and other whole a-b layers of "B", and the ordering
> of
> these layers along "c" is fairly random. Colin just described this
> as a
> "stacking disorder" which is probably a good name for it.
>
> The final case is when A and B are completely uncorrelated and occur
> absolutely at random locations in your crystal. In this case the
> "supercell" can be anything and the "streaks" are in every direction
> (including every diagonal) so they simply show up as increased
> background. Every crystal does this. In fact, this is the origin of
> the B-factor as no two unit cells are exactly alike. Ever wonder
> where
> those photons go that scatter off protein atoms but don't go into
> spots? They go into the background.
>
> Now, since these streaks represent correlations of neighboring unit
> cells this means that the diffuse scattering can tell you something
> about how your molecule moves. There is something about your
> structure
> that forces its neighbors to be the same in at least one direction.
> There are a class of people who study this for a living. I am not one
> of them.
>
> BTW. This is definitely NOT a mosaic spread. Mosaicity occurs on
> length scales thousands of times larger than this. By definition, a
> mosaic spread is the width of the distribution of relative rotation
> angles of "mosaic domains" and these domains all scatter independently
> of each other. An infinite mosaic spread (or at least 180 degrees)
> corresponds to a powder diffraction pattern, and the fact that powder
> lines are sharp demonstrates how mosaicity cannot smear spots in
> anything but the "tangential" direction. That is, no rotation can
> change the d-spacing of a spot. Changes in unit cell size can do
> this,
> but that is a very different phenomenon than mosaic spread as mosaic
> domains are much much bigger than unit cells.
>
>
> The good news is, it is highly unlikely that this will prevent you
> from
> solving the structure. Indeed I think there are many structures in
> the
> PDB that had streaks in their diffraction pattern like this. The
> reason
> it won't hurt you is that the intensity of the Bragg peaks is the same
> in the perfectly-correlated, partially-correlated and completely
> uncorrelated cases. The electron density will simply have a two-
> headed
> side chain in it.
>
> So, I would suggest doing what most crystallographers do and
> completely
> ignore any potentially informative weirdness along the way and sally
> forth. But save these pictures (and the above book) for when your
> reviewer tells you your R-merge is too high.
>
> -James Holton
> MAD Scientist
>
>
> Margriet Ovaere wrote:
>> Dear all,
>>
>> In the diffraction pattern of crystals of an RNA decamer, small lines
>> appeared (see pictures attached). We've tried different crystals but
>> they all showed the same small lines. Has anybody seen
>> this phenomena before and has got an explanation for it please..?
>>
>> Many thanks
>>
>> Margriet Ovaere
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------
>>
>>
>> Margriet Ovaere
>> Chemistry Department K.U.Leuven
>> Biomolecular Architecture
>> Celestijnenlaan 200 F
>> B-3001 Heverlee (Leuven)
>> Tel: +32(0)16327477
>>
>>
>>

-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Biochemistry and Molecular Biology, W8708
615 North Wolfe Street
Baltimore, MD 21205
Phone: +1-410-614-4742
Fax: +1-410-955-3655

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: small lines in diffraction pattern
From: Robert Sweet rsweet {- at -} BNL {- dot -} GOV
Date: 2009-01-28

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Subject: Re: small lines in diffraction pattern
From: Robert Sweet rsweet {- at -} BNL {- dot -} GOV
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