The temperature factor, also called the B-factor, is calculated during the refinement of the structure. The temperature factor for an atom is defined through its mean displacement from an average position:
, where x is the mean displacement of the atom.
For proteins, the normal range of B is around 12 Å2
to 20 Å2
, which corresponds to displacements in the range of 0.15 Å to 0.5 Å. However, higher B values, like 60 Å2
to 70 Å2
, are not unusual. For low resolution structures, these values are usually higher.
Almost all graphic programs for displaying protein structures have the option of coloring the structure according to temperature factors. The regions of high flexibility (high B-factors) are then shown in red, while the low B-factor regions are colored in blue. This feature is useful when assessing the quality of different parts of the structure. Usually, high-B regions are more flexible and, as a result, have weak electron density. Model building in such regions may be challenging and result in a low-quality model for that region. In the PDB file
, each atom's B-factor is the last number in the respective row.
The parameters described here are associated with the X-ray experiment and are unique for crystallographic structures.