Dear Florian,
There have been previous examples where there are distinct
“layers” of protein packing without any obvious density linking the layers, as
it appears in the image you show. One is tyrosyl tRNA synthetase, where the
layers were in fact linked by a disordered domain for which there was no
density. Does the density that you see account for the entire protein (or
complex) that you have crystallised?
I am fairly sure that this has also been seen for membrane proteins, where the
extra-membrane component (or an additional protein, eg a Fab) has been
disordered, again giving layers of density that appear unconnected.
I’m not sure what you mean by “having two distinct lattices”. Do the
diffraction images show any signs of disorder, eg diffuse streaking or features
that are not accounted for by the lattice used when integrating the data?
Best wishes,
Andrew
> On 21 Jul 2022, at 19:29, Schubot, Florian <fschu...@vt.edu> wrote:
>
> Hi, I have a high-resolution data set ~1.6 Angst.) for a twinned crystal (SG
> C2, twin law h,-k,-l). The structure was solved via molecular replacement.
> The map and model look excellent but R and Rfree continue to hover around
> 30%. I do use twinned refinement. Reviewing the packing, I noticed a huge gap
> between layers (picture below). There is NO additional well-defined protein
> density in this gap. I this gap is a symptom of having two distinct lattices.
> I was curious if anyone could advise/comment.
> Thank you,
> Florian
>
> <image.png>
>
> =========================================================
> Florian Schubot, Ph.D.
>
> Associate Professor
> Virginia Polytechnic Institute and State University
> Department of Biological Sciences
> 5002 Derring Hall
> 926 West Campus Dr
> Blacksburg, VA 24061
> United States
> E-mail: fschu...@vt.edu <mailto:fschu...@vt.edu>
> Phone: (540) 231-2393
> Fax: (540) 231.4043
> http://www.faculty.biol.vt.edu/schubot/
> <http://www.faculty.biol.vt.edu/schubot/>
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