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 /
