The B-factor, also called the temperature factor, is one of the many parameters used to fit a potential structure to the electron density map obtained from X-ray crystallography. The diffraction pattern of a crystal of molecules will be affected by the vibration of atoms or molecules within the crystal. During the refinement process, a B-factor is fit to the data in order to account for the 'blurriness' of the electron density due to thermal motion.

If one considers the B-factor to simply be an indication of thermal motion, described as a harmonic oscillator (i.e. isotropic vibration), the relationship between B-factor and displacement is:

B = 8 pi2 u2

Which is equivalent to 79u2. So if the B-factor for a particular atom is 79Å2, then the mean displacement is 1 Å.

Generally, B values are too large to represent thermal motion within a well ordered structure and also reflect disorder of the protein in that region. Generally, one will find the B-factors of sidechains (5 to 60 Å2 to be larger and more variable than backbone atoms (5 to 35 Å2 .