Structure files contain Cartesian coordinates of all the atoms that could be located (modeled) in the electron density map. X-ray crystallographic data also include a temperature factor for each atom in the file. The temperature factor indicates how much an atom oscillates or vibrates around the position specified in the model. In other words, it's a measure of the thermal motion of individual atoms in the crystal. So there are "cold" atoms, with limited motion relative to "hot" atoms with a wider range of motions even in the crystalline state. Chime shows cold atoms in blue and hot atoms in red. Relative values are from red to blue, in order of decreasing temperature. In general, side chains have higher temperatures than backbone atoms.
Aside from several side chains which have high temperatures comparable to the atoms in the N-terminal domain, most of the atoms in the C-terminal domain are "cooler" (see spacefilled model). The average main chain temperature factor for the N-terminal domain is 85 Å2, compared to 40 Å2 for the C-terminal domain. The rigidity of the C-terminal domain stems in large part from the shape complementarity between the protein and RNA contact surfaces.