I believe that the definition of "significant" for crystallographic
data should be based on the difference map. If a shift of that magnitude
causes a feature to appear in the map, then the crystal data is driving
the shift. If you can have a shift that large, for the particular atoms
in question, and the difference map remains flat then the crystal data
doesn't care.
A refinement program will move an atom for lots of reasons in
addition to the diffraction data, sometimes for no reason at all (simulated
annealing, for example). The difference map is a pure expression of the
will of the diffraction data.
The most sensitive calculation is the F(holo)-F(apo) map, but this
requires isomorphous crystals. It might be possible to paste into the
holo model a couple residues from the apo model, refine all parameters
except the position of these atoms, and see if the Fo-Fc map objects.
Remember, a lysine on the surface can probably be built in twenty
different conformations and the difference map flat in every case while
a couple atoms elsewhere could have a shift of 0.1 A that lights up the
map. There are no generic "cut-offs" or "thresholds" that work.
Dale Tronrud
On 9/10/2012 9:01 PM, Michael Murphy wrote:
I am trying to compare structures of the same protein in the apo form and when
bound to several different ligands. There are
differences, but they are subtle and I am unsure whether they are actually
significant or just do to coordinate error or something
similar. Is there a theoretical minimum (in Angstroms maybe?) that a side chain
or secondary structure element needs to be displaced
by between structures to be considered to be "real"? This may depend on
resolution/B-factors as well? Phenix reports overall
coordinate error for each structure, but this must vary for at least a bit for
certain amino acid residues just like B-factors do.
