A Statistical Overview of Experimentally Defined Anisotropic Displacement Parameters (ADP) Currently Deposited in the RCSB PDB

Abstract

The potential of X-ray crystallography to provide information for protein dynamics has not yet been extensively investigated. In addition to atom XYZ coordinates, typical PDB files provide the temperature factor, also referred to as isotropic B-factor, which describes the magnitude of atomic fluctuations. Currently, approximately 5% (∼5500 unique pdb files) of the structures deposited in the RCSB PDB are high resolution (< 1.4 A). These high resolution structures generally provide an additional line for each atom entry, with the second containing a symmetric tensor with six integers that describes an ellipsoidal, instead of spherical, distribution of electron densities. Importantly, this asymmetric distribution of electron density reflects the anisotropic movement of the atomic nuclei. A diagonalization of this 3x3 tensor yields three eigenvalues (W1, W2, and W3), which define the distribution of electron density along those three prominent axes. The degree of anisotropy is defined as the ratio of W1 to W3 and varies between 0 (extremely anisotropic, like a rod or a pancake) and 1 (a sphere). Our preliminary analysis over the ADPs derived from ∼1500 high resolution structures revealed that interestingly, the backbone carbon atoms are more anisotropic than the C-α and C-β atoms. The C-α atoms show the lowest degree of anisotropy, and proceeding out along the side chain from C-α to C-e, the degree of anisotropy gradually increases. We also analyzed the trend of isotropic B-factors. Indeed, the value of isotropic B-factors increases outward from the backbone C to the C-e atom. In summary, we performed a statistical analysis over the ADPs of structures in the RCSB PDB, with the aim to obtain useful information in order to gain a better understanding of the physical basis of ADP.