The reason is that you've missed out one important term: the atomic displacement parameters (B-factors), which describe a combination of thermal motion and positional disorder between unit cells.
A somewhat niggling point: isn't it true that the thermal motion is insignificant at 100K? Does anybody know of a paper which systematically measures B-factors as a function of temperature? The asymptote of the resulting curve would represent all of the non-thermal elements, right?
JPK
