Colin Nave wrote:
..
>
> Also Acta Cryst. (2002). D58, 29-38 "The 2.6 Å resolution structure of Rhodobacter capsulatus bacterioferritin with metal-free dinuclear site and heme iron in a crystallographic `special position' "D. Cobessi, L.-S. Huang, M. Ban, N. G. Pon, F. Daldal and E. A. Berry ( http://scripts.iucr.org/cgi-bin/paper?S0907444901017267 ) though the 'special position' is justifiably in quotation marks in this example as disorder is present.
>
> Colin
>
Yes, this was an example of Ian's "rotationally disordered with occupancy 0.5"
possibility.
Heme has a pseudo-two-fold axis passing through the plane of the ring,
which is violated only by the position of the methyl and vinyl substituents
on either side: rotating through the pseudo-2-fold superimposes methyl on
vinyl and vice versa on either side. This axis was sitting on a
crystallographic 2-fold.
We did trial refinements in a lower symmetry space group so the
axis became NCS, and we refined with the heme in one orientation or
the other. In either case, difference maps showed positive density
for another atom beyond the methyl, and negative density on CB of
the vinyl. So we concluded the heme was oriented both ways, and
in the average satisfied the symmetry of the higher space group.
Putting it with half occupancy in the asymmetric unit allowed
crystallographic symmetry to generate the rotated half.
Looking at it from the heme's point of view, this makes sense.
Its environment is perfectly symmetrical, so there is no way
for it to choose one orientation over the other and both are
adopted equally. (The two-fold is intrinsic to the "biological unit",
not generated by crystal packing).
I think the heme iron was right on the crystallographic axis.
When refining in the lower space-group with two .5 occupancy
non-interacting hemes, the propionates (which actually satisfy the
covalent symmetry) in the two hemes took on different conformations,
not sure if this was significant or just "taking liberties where
freedom is given".
eab
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