What is the resolution of your data? I have been able to get a solution for
my protein with 30% identity but my resolution of data was 1.4 Angs. I
believe to get a solution at 18% identity your search model has to be very
close, like using Robetta to make the 3 mer and 9mer peptides and then work
f
Dear Ursula,
18% identity is really in the twilight zone for molecular replacement, where it
may work but there are certainly no guarantees.
However, there’s a feature in Phaser that is useful for this kind of problem,
i.e. the “rotate around” option, where you take advantage of knowing the
ap
Dear Jose
Your email expressed far more clearly than mine the problem
of symmetry, and I had completely forgotten this discussion in the
classic MWC paper. The point about measuring the molecular weight in
solution is to find IF the protein forms an oligomer or not - AUC
can give some idea of sha
Hi Ursula,
I also tried to just superimpose the complete model onto the partial
> solution. This results in quite nice packing, but doesn't refine. Is there
> a rigid program refinement program with very large convergence?
>
depending on what you call "very large", this may be helpful:
Automat
I am trying molecular replacement with a very poor model. The model
consists mainly of 1 long helix and two slightly bent antiparallel helices.
After dividing it into 2 fragments, I was able to find a solution for one
of the fragments ( at least I think so after looking at maps, packing,
refinement
Hi everyone,
Just wanted to second the SAXS suggestion:
the approach should provide a very rigorous way of testing the candidate models
apparent in the crystallographic lattice, and can assist with questions of
mass. (among the most common applications)
With regards to the mass questi
Hi Hay,
I think SAXS should be more than capable of discriminating between a 12.5
kDa monomer vs ~37.5 kDa trimer.
Lysozyme is a useful standard used in SAXS (as with most structural
biology!), and Lysozyme is only slightly larger than your proteins.
Cheers,
Dave
On Fri Dec 12 2014 at 5:13:26
Tanner:
Thanks, GREAT reference on asymmetric homo oligomers!
SAXS sounds like a good idea for a bit larger particles. I'm afraid it might
be very difficult to get enough resolution to resolve oligomerization of a
rather small 12.5 kDa protein like ours, but will look into it more closely.
Joes
Two thoughts on asymmetric oligomers.
1. Here is a recent survey of asymmetric homodimers in the PDB. I know you
are looking for trimers, but at least this provides a precedent for asymmetric
oligomers.
Swapna LS, Srikeerthana K, Srinivasan N. Extent of structural asymmetry in
homodimeric pro
Dear all,
PETRA III will restart next spring and we are looking for people
to join the EMBL team operating and developing the P13/P14
beamlines and related facilities. The positions available comprise
user support and the possibility to carry out research projects.
EMBL and the DESY Campus offe
Dear Hay
Your post prompted me to respond, since I think the issue of symmetry is
extremely important.
I would like to reinstate here what should be obvious to everyone: a
stable asymmetric assembly of proteins in solution is essentially
impossible (or at most very very unlikely), purely bec
Dear Jeremy,
Indeed, we also incline to think of it as a monomer in solution, but still
quite un-eased by the extensive interactions in the asu being merely as a
result of a crystallization artifact. As you said, we may need to rely more
heavily on biochemical analysis and since SEC wasn't clea
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