As others have said, we struggle to parameterise models at lower
resolutions. There are doubtless multiple models and not much data to
test these against..
Anisotropic ellipsoids or TLS and other schemes such as torsion angle
refinement are all approximations to reality at low resolution - as
Gerard says there are multiple conformations which are approximated by
these parameterisations, but there are some advantages in keeping the
number of parameters to a minimum.
I assume we all agree that the point of refinement at a low resolution
is to to improve the electron density to reveal more detailed features,
and I feel that such improvement is quite closely linked to reducing the
FreeR, and I would choose a relative weighting scheme between X-ray and
restraints which would give the lowest FreeR . Trying to deduce RMSDs
on bonds for an X-ray structure where the density appears as a sausage
is pretty meaningless
Eleanor
George M. Sheldrick wrote:
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Ethan Merritt wrote:
However, when individual atoms are modelled anisotropically, there
is an apparent bond-length compression that arises from failing to
apply a correction to the distance between the centroids of two
ellipsoids. Programs such as shelx apply this correction when
reporting bond lengths.
Ethan,
To put the record straight, shelxl does not correct bond lengths for
libration, but a program I wrote many years ago (called xp) that is
still sometimes used by small-molecule crystallographers does.
In fact the correction is negligible for large molecules, but is
important for small molecules and ions such as sulfate and phosphate
that one often needs to handle in protein structures. For this reason
I do not recommend restraining the bond lengths in these ions to
particular target values (DFIX in shelxl) but prefer to apply the
restraints that e.g. all S-O distances are equal and all O..(S)..O
distances are equal (SADI in shelxl). This also takes into account the
effect of pH on the P-O distances in phosphates! Alternatively in
shelxl one can apply the 'variable metric' rigid group constraint
(AFIX 9) that keeps the angles and the relative bond lengths fixed but
allows the group to shrink (or expand) as a whole.
George
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