The Meaning of Temperature factors

Temperature factors are properties of the crystal structure of macromolecules. They can signify one of two things:

  1. They are a measure of the relative stability a local area of a macromolecule. Since the pattern on the detector screen is a taken over a period of a few days, the coordinates of the atom are found by taking a time-average of the diffraction pattern. A low temperature factor indicates a section with values with a fairly narrow distribution, and this signifies relatively little movement of that part of the molecule in the crystal. A high value can signify a wide distribution of positional values for that particular section of the macromolecule. This means that the section in question is moving around more rapidly in the crystals.

  2. High temperature factors can also represent errors or uncertainty in the refinement of the diffraction patterns into 3d coordinates of the macromolecule.
The units used for temperature factors are angstroms^2, and the values encountered can range from 0-100. A value of 10 is about average, 50 indicates lots of movement, and values 90-100 usually indicates error or major uncertainty in the refinement of the crystallographic molecular model.

The color scale on the graphics goes from blue, representing low temperature factors, to green representing median temperature factors, to red representing high temperature factors.

It should be noted that the scale is extrapolated based on the maximum and minimum values present in each individual protein. As such, the scale varies slightly from molecule to molecule. These plots give a good comparison of temperature factors among the residues of each protein, but is only a good as a very general comparison between the different proteins.