The average atomic volume and density of proteins

Abstract

Abstract The density of proteins is an important quantity. For ab initio phasing in X-ray crystallography, such as low resolution envelope techniques [1, 2], an accurate protein density is essential to get a correct prediction of the protein volume from the amino acid sequence. An accurate value will also facilitate the determination of the number of protein subunits in the unit cell. There has long been a general consensus that the mean density of a protein is 1.35 g/cm3 [3], but this value should be revised. The present study, based on X-ray crystallographic coordinates of 28 different proteins, shows that the mean density of proteins is 1.22 ± 0.02 g/cm3. The protein density was calculated using the Voronoi construction with over 80% of the total number of atoms in the protein molecules taken into account.