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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