Temperature value: Difference between revisions

In [[X-ray crystallography|crystallography]], '''uncertainty''' in the positions of atoms increases with '''disorder''' in the protein crystal. Disorder may have two components, static and dynamic. [[Resolution]] represents the average uncertainty for all atoms. In contrast, the ''temperature value'' (also called ''temperature factor'' or ''B factor'') quantitates the local uncertainty for each atom. A high temperature factor reflects a low [[electron density]] for the atom, and ''vice versa''. The temperature value is recorded in the [[atomic coordinate file]]. In the [[PDB format]], it is the last numeric value (columns 61-66) in each ATOM and HETATM record.

In crystallography, '''uncertainty''' in the positions of atoms increases with '''disorder''' in the protein crystal. Disorder may have two components, static and dynamic. First, some regions of the molecule may adopt different conformations in different copies of the molecule, each molecule's conformation being relatively stable (static disorder). Second, some regions of every copy of the molecule may be subject to thermal motion, meaning vibration about the rest position (dynamic disorder)<ref>[http://www.elsevier.com/wps/product/cws_home/707331 Rhodes, G. 2006. Crystallography Made Crystal Clear, 3rd ed. Academic Press.]</ref>. Large thermal motions cease when the crystal is frozen very rapidly with liquid nitrogen, which is the usual procedure prior to irradiation. Typically, protein crystals are kept well below freezing while being irradiated, although irradiation may warm the crystal permitting some thermal motion. Disorder in a frozen protein crystal may include both static disorder and dynamic disorder, the latter being represented by the "snapshot" of thermal disorder frozen in a moment in time.

Some regions of the molecule may have higher average disorder, and others lower average disorder. Typically, the ends of chains have higher average disorder, and hence their positions are less certain than are residues in the core of a tightly packed domain, where disorder is less. The disorder for each atom is quantitated in its '''temperature factor''' also called ''B factor''.