Dear Dr Cowtan
Thankyou for your considered and considerate posting today. Your
explanation of the implications of the use of MAD, heavy atoms and phasing
is especially helpful. I have come to think that the process of
oligonucleotide structure refinement may not actually be the basic source of
the structural difficulty which exercises me, even in those algorithms where
only a double helical outcome is allowed.
In the various discussions which are currently in progress in this
newsgroup, and in bionet.xtallography, I think I am now better able to focus
on the issue in oligonucleotide crystallography which I need to have
resolved. I would be very glad to have your opinion.
The sample of references I include here all relate to studies in
oligonucleotide diffraction where patterns of systematic absence, or
patterns of systematic absence plus weak presences, would allow the choice
of a unit cell of smaller cross-section than the researchers actually chose
(in order to accord with unit cell dimensions originating with the early
fibre diffraction studies (which themselves often show the same patterns!)).
Am I right to think that, were the smaller unit cell dimensions to be used
in the deconvolution of the structure factor files, perhaps re-indexing as
necessary, and whether using MAD, heavy atoms, etc., the resulting
Pattersons would merely emerge with smaller scales on their X,Y axes ?
Could not the phasing process and subsequent unbiased refinement be carried
out equally well on the smaller unit cell, but inevitably result in a
different structure ?
Clive Delmonte
1 Molecular Structure of d(GTGTACAC) in the spermine-bound
tetragonal and the spermine-free hexagonal crystal forms; Sanjeev Jain, PhD
Thesis; University of Wisconsin at Madison (1990)
2 Double helix conformation, groove dimensions & ligand binding
potential of a G/C stretch in B-DNA; Udo Heinemann, Claudia Alings & Manju
Bansal; The EMBO J Vol 11 (1992) 1931 - 1939
3 Unusual helical packing in crystals of DNA bearing a mutation hot
spot; Y Timsit et al.; Nature Vol 341 (1989) 459 - 462
4 A Salt-induced Conformational Change in Crystals of the
Synthetic Tetramer d(CGCG); H.R. Drew, R.E. Dickerson & K. Itakura; J Mol
Biol Vol 125 (1978) 535 - 543
5 The Crystal & Molecular Structure of a Calcium Salt of
Guanylyl-3',5'-Cytidine (GpC); B. Hingerty et al.; Acta Cryst. B32 (1976)
2998 - 3013
>Dr. Kevin Cowtan, Structural Biology Laboratory, University of York, UK
