On 04/07/2014 03:16 PM, Eugene Valkov wrote:
Thanks for the input, Eugene. No, these do not impact phasing or
refinement significantly. We've SAD phased data like these with 5-Br and
5-I dU with no problems. The refinement is a bit tricky for some of the
structures because they are lower resolution and the space group is
pretty small, but that isn't related to the streakiness.
--p
Paul,
The fibre-like characteristics present in some diffraction patterns of
nucleic acids, which I think you are referring to, is the contribution
of the helical transform of the double-stranded helix. Essentially,
the length of the regular spacings in the base pairs modulates the
intensities of the Bragg reflections. These then do not decay smoothly
as the function of resolution which results in intensities along the
helical axes at 3.4A being quite strong whilst perpendicular ones are
much weaker. I have observed this in the diffraction patterns of RNA
crystals but I have not seen the diffuse streaking along lattice lines
that you show.
One recent example of fibre-like diffraction of a nucleic acid is
illustrated here:
https://drive.google.com/file/d/0B-wXJqcqFfUHUVpvZDhqREdqMzA/edit?usp=sharing
I do not think that what you are seeing in your crystals can be
attributed solely to the above. The streaking between the spots is
probably some sort of lattice anomaly. It would be interesting to hear
if this had impacted in some way on phasing or refinement of the
structure.
Eugene
On 7 April 2014 19:03, Paul Paukstelis <shocksofmig...@gmail.com
<mailto:shocksofmig...@gmail.com>> wrote:
Seeing the diffuse streaking threads that have cropped up recently
got me to thinking about many of the DNA data sets we have
collected on. We always see diffuse streaking along lattice lines.
See images:
http://vespa.chem.umd.edu/~paul/hex_streak01.png
<http://vespa.chem.umd.edu/%7Epaul/hex_streak01.png>
http://vespa.chem.umd.edu/~paul/hex_streak02.png
<http://vespa.chem.umd.edu/%7Epaul/hex_streak02.png>
http://vespa.chem.umd.edu/~paul/hex_streak03.png
<http://vespa.chem.umd.edu/%7Epaul/hex_streak03.png>
My original interpretation of this as fiber diffraction from
alignment of DNA bases came after reading Doucet et al. Nature
337, 190-192 and seeing that the streaks start at around 3.4A and
orientation of the helical portions of the structure are
perpendicular to the six-fold. I didn't really give it much more
thought till seeing the threads about diffuse streaking. These
show up even in crystals that diffract to higher resolution than
the one shown in the images. I wonder if this is actually
something else given that they are along lattice lines? Opinions?
--paul
--
Dr Eugene Valkov
Room 3N049
Division of Structural Studies
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
Email: eval...@mrc-lmb.cam.ac.uk <mailto:eval...@mrc-lmb.cam.ac.uk>
Tel: +44 (0) 1223 267358
