On Wednesday, 27 May 2020 18:49:23 PDT Jessica Bruhn wrote:
> Hello,
>
> I am wondering if pseudosymmetry can cause weak reflections that mimic the
> doubling of one unit cell axis' length. Has anyone seen something like this
> before?
Yes.
> I am processing data from a small molecule sample collected with electron
> diffraction from multiple crystals. For the b axis, it is not clear if the
> length should be 10A or 20A. There are spots with the correct spacing for
> b=20A, but every other spot seems weaker than the spots along k if I choose
> b=10A (this extends beyond (0,k,0)). I am unable to phase the b=20 data. I
> have solved this structure in P1 with b=10 and found four molecules in the
> ASU and in P212121 with b=10 resulting in one molecule in the ASU.
> In P1, three of the four molecules adopt the same conformation, but the fourth
> molecule is in an alternate conformation that causes only ~1/2 of the
> molecule to be consistent with the first three. In P212121 I see density
> for part of this alternative conformation, but the full molecule in this
> alternate conformation cannot pack properly in P212121. Based on these
> results and some orthogonal data, I think I should refine the solution in
> P1 with b=10. Does it seem reasonable that pseudosymmetry is causing these
> weak reflections along k hinting at a doubling of the b axis?
This description makes me think also of a supercell. This can happen
when, say, the position of one copy N is not compatible with all (N-1) of
the others positions. Some unit cells contain (N-1) copies but not the
problematic N; other cells contain the N copy but miss one or more of
the others to make room. This gives you a stochastic mix of cell
contents. If it were truly random you'd see spots for a small cell
but the contents would have to be described by partially occupied sites.
But if there is a bias towards alternation of cells +N -N +N -N you
get a pseudo-doubling of that cell edge, matching your description.
Suggested reading:
Lovelace J, Petrícek V, Murshudov G, Borgstahl GEO.
Supercell refinement: a cautionary tale. Acta Crystallogr D Struct Biol. 2019
Sep 1;75(Pt 9):852-860.
doi: 10.1107/S2059798319011082. Epub 2019 Aug 28. PMID: 31478908; PMCID:
PMC6719663.
I've had to deal with these in macromolecular crystals.
I would imagine that the same can happen for electron diffraction
but I can't point to any prior examples in the literature.
good luck!
Ethan
> Thanks in advance!
>
> Best,
> Jessica
>
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
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