Dear Ed, You might well have a case of something called "lattice-translocation disorder", which is indeed an intermediate type of disorder with partially coherent interference between crystal domains related by non-lattice translations. Take a look at a recent paper on the subject (for instance, Acta Cryst. D65, 980-988) and at the references in it. This type of disorder has a long and distinguished history in protein crystallography, starting with a paper by Bragg & Howells in 1954 (Acta Cryst. 7, 409-411).
Good luck! Gerard. -- On Fri, Oct 15, 2010 at 06:08:09PM -0400, Ed Pozharski wrote: > A couple of twinning-related questions. > > I have a protein-DNA complex in P65. Protein binds DNA as a dimer, DNA > itself is not palindromic and has sticky ends located asymmetrically > with respect to the protein (dimer). > > DNA contains a single fluoro-uracil which is flipped into the active > site. This 3A structure can be easily refined down to Rf~35%, at which > point difference density tracing the fluoroU and adjacent basepairs of a > "self-superimposed" dimer is visible in the active site of the second > monomer. > > The dimer two-fold axis are aligned with the bisector of the (a,b). > Thus my first question - do I understand correctly that this corresponds > exactly to (k,h,-l) operator which is one of the possible twinning > operators in P65? > > When I try twin refinement in Refmac, the Rfree drops some 3% and > reported twinning fraction is 10%. It's great to have the lower Rfree, > of course, but I doubt that 10% occupancy would give me a detectable > density (I see mainly phosphate, but the fluoro-U moiety is rather clear > too). And indeed, the difference density remains after accounting for > twinning. > > So I tried the "dual model", where I have two copies of the whole > assembly, with the second one obtained by rotation around dimer axis. > The Rfree drops another 3%, and the difference density is now accounted > for, but the occupancy optimized for the lowest Rfree is about 50%. > > Thus my second question - since twinning appears to be related to the > same spatial transformation, why it doesn't account for it? And in more > general sense - what is going on in this lattice? > > Afaiu, the twinning and dual model contribute to the Fc in different > ways. For twinning part, the Fc=sqrt(|F1|^2+|F2|^2), whereas for dual > model Fc=F1+F2 with phases included. Now, does this mean that I somehow > have two types of twinning in this crystal - "coherent" (at 50%) and > incoherent (at 10%)? Or is it that both description are correlated - in > which case I don't understand why I get an additional drop when the two > are combined. > > It may also be important that two-fold dimer axis are not exactly (but > close) at the bisector - the polar angles reported by superpose are > (87.91,-116.242,179.987). > > I'll appreciate any suggestions, > > Ed. > > -- > Edwin Pozharski, PhD, Assistant Professor > University of Maryland, Baltimore > ---------------------------------------------- > When the Way is forgotten duty and justice appear; > Then knowledge and wisdom are born along with hypocrisy. > When harmonious relationships dissolve then respect and devotion arise; > When a nation falls to chaos then loyalty and patriotism are born. > ------------------------------ / Lao Tse / -- =============================================================== * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===============================================================