Bfactors

B factors, also called temperature factors or atomic displacement parameters (ADP), are numerical values used in X-ray crystallography and related methods to describe the attenuation of scattering due to atomic displacement from thermal motion and static disorder. They are assigned on a per-atom basis in a structural model and reported in PDB files as B values. The B factor is related to the mean square displacement by B = 8π^2 ⟨u^2⟩.

Higher B-values imply greater positional uncertainty; atoms in flexible parts of the molecule, solvent molecules, or partially occupied sites often have high B-values, while atoms in well-ordered cores or bound metal ions tend to have lower B-values. B-values reflect both real thermal motion and static disorder and can be influenced by data quality, model accuracy, and occupancy. Refinement strategies may use global models such as TLS (translation, libration, screw) to describe collective motion instead of per-atom B-values.

In refinement, B factors can be isotropic (the same value in all directions) or anisotropic (a six-parameter tensor), with anisotropic refinement requiring higher data quality and more parameters. The Debye–Waller factor exp(-B sin^2 θ / λ^2) modulates observed diffraction amplitudes, linking B to measured intensities. Practically, B-values are used to assess model quality, guide model building, and visualize regions of flexibility; they can also indicate disorder or partial occupancy when interpreted, so they are considered alongside occupancy and other refinement parameters.