From owner-biophysics@net.bio.net Wed Feb 10 22:00:00 1999 From: "Clive Delmonte" Newsgroups: bionet.biophysics,bionet.xtallography References: <36b81714.0@news.netdirect.net.uk> <36BE3682.977F323B@bioreason.com> <36beffa3.0@news.netdirect.net.uk> <36C2F730.D63B2951@yorvic.york.ac.uk> Subject: Re: Is ignorant rambling, was: DNA Structure: An Age of Refinement... Date: Thu, 11 Feb 1999 20:30:39 -0000 Lines: 55 X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 NNTP-Posting-Host: 195.7.225.36 Message-ID: <36c33934.0@news.netdirect.net.uk> X-Trace: 11 Feb 1999 20:10:28 GMT, 195.7.225.36 Path: biosci!agate!newsfeed.berkeley.edu!newshub.northeast.verio.net!btnet-peer!btnet!newspeer.clara.net!news.clara.net!peer.news.nildram.co.uk!news-peer.netdirect.net.uk!news.netdirect.net.uk!195.7.225.36 Xref: biosci bionet.biophysics:4780 bionet.xtallography:4596 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 .