Do the mass spec of your crystal to identify the other protein. Once done
solve your structure and build the complete model. This should be straight
forward and quick.
Best Wishes
On Sat, 4 Nov 2023, 09:05 Sam Tang, wrote:
> Dear community,
>
> I am solving the structure of a complex between
IF your MR solution is correct ( ie r factor falls on refinement to 40%
say) and your protein A is roughly 50% of the complex, and IF your data is
good to 1.9A (assumed SG correct etc) I would do my best to correct any
obvious rebuilding needed for protein A, ( r factor should fall further if
this
Hi,
At 1.9A resolution there should be lots of possibilities, depending on the
details.
You imply you have partial sequence information for chain B. Is there a genome
for your plant or a relative of it? You could search for possible matches to
your sequence, and then test all the AlphaFold
On 04/11/2023 14:04, Sam Tang wrote:
Dear community,
I am solving the structure of a complex between proteins A and B,
where A is a protein with known homologs and B is a novel protein
isolated from plant. The diffraction data was at 1.9 Ang collected
in-house, indexed to P321. Using A as
What Oleg says is right. The phases may be too poor to Bootstrap from. Oleg
also reminded me that the MR solution may be incorrect. I would check the
following:
What were the TFZ and LLK scores for the MR solution (if you used Phaser
for MR)?
What are the R-factors after molecular replacement?
Hi Sam,
ARP/wARP should work well at 1.9A resolution. If it did not then there are
things to check such as whether the space group is correct and whether
there are major deviations in the Wilson plot.
Do you have a suspected sequence for chain B? If so, I would provide that
to the programs to
Sam,
>From what you wrote, it seems that the best thing is to build manually and
>iteratively, at least at the beginning, starting with building the A chain as
>well as you can and build parts of B as you go. MR phase has bias, of course,
>so the only way is to do this is in many iterations.
I
Dear community,
I am solving the structure of a complex between proteins A and B, where A
is a protein with known homologs and B is a novel protein isolated from
plant. The diffraction data was at 1.9 Ang collected in-house, indexed to
P321. Using A as the search model, we have got a reasonable
