Thanks Diana - Indexing on strong reflections (STRONG_PIXEL=50 in xds) does
identify C222 as a possibility with the same dimensions as the P222 cell.
This doesn't solve my problem, though, since the centering operation just
replaces the tNCS and doesn't relieve the crowding.
Best wishes
Kevin
--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431
On Fri, May 31, 2019 at 1:35 PM Diana Tomchick <
diana.tomch...@utsouthwestern.edu> wrote:
> Your native Patterson indicates pseudo C-centering. Are you sure you don’t
> have space group C222(1)?
>
> If your space group is correct, it’s still pseudo C-centered. You should
> see that in the intensity-weighted reciprocal lattice.
>
> You could try re-indexing on just the most intense spots to give you a
> data set indexed in a C-centered lattice. Use that data to solve via MR,
> then convert to the data indexed in the actual space group.
>
> Diana
>
> **************************************************
> Diana R. Tomchick
> Professor
> Departments of Biophysics and Biochemistry
> UT Southwestern Medical Center
> 5323 Harry Hines Blvd.
> Rm. ND10.214A
> Dallas, TX 75390-8816
> diana.tomch...@utsouthwestern.edu
> (214) 645-6383 (phone)
> (214) 645-6353 (fax)
>
> On May 31, 2019, at 3:09 PM, Kevin Jude <kj...@stanford.edu> wrote:
>
> Hello community, I wonder if I could solicit advice about a problematic
> dataset. I plan to solve the structure by molecular replacement and expect
> that the protein is relatively compact, ie not elongated. SAXS data
> supports this expectation.
>
> The crystals diffract to 2.6 Å resolution and appear to be in P 21 21 2
> with a = 49, b = 67, c = 94, which should fit <=2 molecules in the ASU with
> 40% solvent. The native Patterson shows a large peak (12 sigma) suggesting
> a tNCS vector of {0.5, 0.5, 0}.
>
> If you're sharper than me, you may have already spotted the problem - c is
> the long axis of the unit cell, but tNCS constrains the proteins to a plane
> parallel to the a,b plane. Indeed, molecular replacement attempts using
> Phaser will not give a solution in any orthorhombic space group unless I
> turn off packing, and then I get large overlaps in the a,b plane and huge
> gaps along c.
>
> Since I believe that my model is good (or at least the correct shape,
> based on SAXS), I wonder if I'm misinterpreting my crystallographic data.
> Any insights into how to approach this problem would be much appreciated.
>
> --
> Kevin Jude, PhD
> Structural Biology Research Specialist, Garcia Lab
> Howard Hughes Medical Institute
> Stanford University School of Medicine
> Beckman B177, 279 Campus Drive, Stanford CA 94305
> Phone: (650) 723-6431
>
>
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