Hi Bob et al:
I think that this is the convolution of the helical transform with the
Bragg diffraction, which you often see in nucleic acid diffraction
patters. I think I first saw it, in fact, at your beam-line in 1994,
with ribozyme crystals. (Aaron Klug had to explain it to me.)
The part that puzzled me was that the dark spots seem to be modulo 10,
whereas for A-form RNA it should be 11 (due to 11 bases per helical
turn). But then I read the initial email, and it says "RNA decamer."
So I think what is happening is that the RNA is slightly distorted to
10 bases per turn to accommodate the crystal lattice repeat. The
horizontal lines aren't "diffuse" scatter, but rather the layer line
scatter of a helical transform described by increasing order
cylindrical Bessel functions (mod 10).
All the best,
Bill
On Jan 28, 2009, at 6:57 PM, Robert Sweet wrote:
I'm coming in late here, having only now found time to look at the
images. It's facinating, isn't it?
Since the lines are not arcs centered on the origin, this isn't
mosaic spread.
For those who haven't seen the image and the zoom, the diffraction
pattern clearly shows one very long axis and a couple of much
shorter ones. The rotation image is taken rotating around the long
one. The small lines are perpendicular to the long axis, and run
fairly continuously, narrowly and evenly spaced at the intervals of
the reflections along this axis, throughout the diffraction pattern.
They're all faint and about the same intensity, and modulated along
their length only slightly. Also it appears that this is a rotation
of about one degree; Margriet doesn't give us clues for any of this.
I'm guessing that whoever said it's a diffuse scatter effect is
close to the mark. I think diffuse scatter comes from the contents
of each unit cell being essentially identical, but that within the
molecule things are waving around a bit (where are Don Caspar and
George Phillips when we need them?), that is, different in each unit
cell. I'll go a touch farther and suggest that it's really disorder
-- each unit cell is well aligned to the others, but each one is
different in a more significant way. I'll guess that the RNA
decamer is aligned along this long unit cell axis, but in some way
either there's an opportunity for the register along the RNA axis to
slip from one unit cell to the other or each is rotated slightly.
On the other hand, the fact that there's a wide distribution of
intensities in the Bragg spots, which are quite sharp, is confusing
-- there must be a lot of contrast in the averaged structure for
this to be true.
Ok, it's interesting, but I have no idea.
Bob
On Wed, 28 Jan 2009, Jacob Keller wrote:
There is something in the unit cell, aligned with the long axis of
the cell, with a periodicity corresponding to ~1/5 of the long
axis. This can be seen as greater intensities along the long axis
every fifth spot. Without knowing the unit cell parameters, I would
guess it is either the interplanar spacings of the nucleotides
(probably this is too small) or the periodic twist of the helix
itself. Interesting that the RNA is a decamer ( = 2 x 5). I would
be curious to know what the unit cell parameters are, or more
generally, what is causing that noticeable periodicity...
Jacob
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
*******************************************
----- Original Message ----- From: "James Holton" <jmhol...@lbl.gov>
To: <CCP4BB@JISCMAIL.AC.UK>
Sent: Wednesday, January 28, 2009 12:20 PM
Subject: Re: [ccp4bb] small lines in diffraction pattern
Hmm. I don't remember that thread. However, I personally think
it is a good idea to keep the "mosaic crystal" as Ewald and Darwin
defined it. Just because current integration software lumps things
together into a "mosaicity" does not mean that every mechanism
contributing to the rocking width of a spot should be given the
same name. Especially when it is difficult to describe the mosaic
crystal using any other words. Perhaps Colin could come up with a
cool word for unit cell non-uniformity? Or is he waiting for us
to name it after him? "Nonuniform Anisotropic Variance of
Elasticity"? or "Cells Of Loose INdex"?
Comments and suggestions are welcome.
-James Holton
MAD Scientist
Jacob Keller wrote:
I had thought that in a previous thread, we had all come to a
consensus that actually the largest source of what is normally
explained as "mosaicity" is really differences in unit cell size,
due perhaps to uneven shrinkage in crystals upon freezing or
otherwise. I believe that there was actually an acta cryst paper
which investigated all of the various ingredients of "mosaicity"
which supports this (this is why I said it.)
Jacob
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu <mailto:j-kell...@northwestern.edu
>
*******************************************
