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>
*******************************************
