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 /
--
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