Dear Florian,
I had a similar case for the membrane protein OmpF where the protein
stacked in columns, linked together by detergent belts acting as glue.
This allowed for 2 disctinct monoclinic space groups, one with tNCS and
the other one without. The detergent allowed for a rotation of a column
building block by 178° (not 180°).
In the discussion of the paper I listed other cases where similar
"absence of lateral packing" have been reported, might be useful for
your situation.
https://pubmed.ncbi.nlm.nih.gov/26620074/
Sorry, no clue about how to reduce your Rs.
Best of luck
Vincent
Le 22/07/2022 à 07:31, Eleanor Dodson a écrit :
Hmmm - is there a smaller lattice which might fit the density? As
Andrew says there are examples of pseudo emptiness in crystals but
there are more examples of wrong lattices!
Check for non-crystallographic translation?
You could attach the pointless/aimless/etc log files..
Eleanor
On Fri, 22 Jul 2022 at 10:15, Andrew Leslie - MRC LMB
<[email protected]> wrote:
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 <[email protected]> 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:[email protected]
Phone: (540) 231-2393
Fax: (540) 231.4043
http://www.faculty.biol.vt.edu/schubot/
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