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.
