Hi,
Lattice-translocation disorder is one possibility.
How does the diffraction image look like?
Are there any streaks?
Best regards,
Takanori Nakane
On 2014-07-30 15:58, Minyun Zhou wrote:
> Dear all,
>
> I am trying to determine the structure of a protein-DNA complex. I
> collected several datasets of the same protein in complex with two
> dsDNAs. Two DNAs have the same sequence, but one DNA contain a single
> central mispair, which is cleaved by the enzyme leaving an abasic
> site, while the other contains a non-cleavable mispair. Two datasets
> have almost the same space group and cell parameter, however, the
> later one has been detected with pseudo-translation while the other
> not.
>
> The details of two datasets are as follows:
>
> Dataset 1. Protein with abasic site containing dsDNA:
>
> C2221: a=106, b=111, c=182.2, α=β=γ=90
>
> Resolution: 2.45 A
>
> Xtriage summary: The largest off-origin peak in the Patterson function
> is 18.57% of the height of the origin peak. No significant
> pseudotranslation is detected.
>
> Dataset 2. Protein with non-cleavable lesion containing dsDNA:
>
> C2221: a=106.1, b=111.1, c=183, α=β=γ=90
>
> Resolution: 3.0 A
>
> Xtriage summary: The analysis of the Patterson function reveals a
> significant off-origin peak that is 60.75 % of the origin peak,
> indicating pseudo translational symmetry.
>
> I first determined the structure using the dataset 1 by MR. There are
> two protein-DNA complexes in one asymmetric unit, and two molecules
> are similar except the conformation of a small loop at the active
> site. The final model has the Rwork/Rfree of 19.3%/23.0%. Then I use
> this refined structure as model to solve the second structure with
> dataset 2. The final Rwork/Rfree is 24.3%/28.9%. The DNA density
> looks okay while the protein part is problematic. After refinement,
> although the main chain of the protein is fitted well into the
> density, there is still a lot of unidentified continuous positive
> density next to the polypeptide chain, especially near the region
> involved in the crystal packing. I attached a snapshot below, which
> shows one of these positive densities lies along a helix. Since there
> is no other polymer in the reservoir solution that can fit, the
> additional density seems to indicate another slightly shifted
> conformation of the protein itself. My question is whether this
> seemingly “dual conformation” is caused by pseudo-translation and
> indicates the solution I found is incorrect. And how can I eliminate
> the effect of pseudo-translation to get the correct structure?
>
> Thanks for your help!
>
> Best regards,
>
> Minyun
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