Correlation coefficient between the ANM and experimental isotropic temperature factors as a function of the ANM cutoff distance using various ways of treating the crystal environment. Each point (*squares*, *circles*, and *triangles*) represents a weighted average for the set of 83 proteins (Eq. ). The solid lines and shapes include all normal modes in the calculations whereas the dashed lines and open shapes include only 5% of the modes for each protein. The squares, circles, and triangles are for the ISL, ASYMPBC, and P1PBC boundary conditions, respectively. Comparing the boundary conditions, including the crystal environment via periodic boundary conditions, clearly improves the agreement with experiment, and the largest gains are at shorter cutoff distance. Both ASYMPBC and P1PBC yield similar agreement for both set of calculations (5% and 100%). As discussed in the text, using 5% of the modes dramatically reduces the agreement, and this behavior has a strong dependence on the cutoff distance.

## PubMed Commons