Table 1. Computation of atom number densities for ribosomes and calcium phosphate.
Element | # of atoms | Mole fraction | # atoms/nm3 | |
---|---|---|---|---|
ribosomal RNA* | C | 68671 | 0.295 | 31.2 |
H | 78158 | 0.336 | 35.5 | |
N | 27884 | 0.120 | 12.7 | |
O | 50462 | 0.217 | 22.9 | |
P | 7216 | 0.031 | 3.3 | |
Mg | 239 | 0.001 | 0.24 | |
Ribosomes† | C | 135061 | 0.186 | 19.3 |
H‡ | 372416 | 0.514 | 53.2 | |
N | 48041 | 0.0663 | 6.86 | |
O‡ | 161037 | 0.222 | 23.0 | |
S | 501 | 0.000692 | 0.072 | |
P | 7216 | 0.00996 | 1.03 | |
Mg | 239 | 0.000330 | 0.034 | |
Ca3(PO4)2 | Ca | 3 | 0.231 | 18.4 |
as crystalline TCP§ | P | 2 | 0.154 | 12.2 |
O | 8 | 0.615 | 49.1 |
* The partial specific volume of RNA was taken to be 0.569 cm3/g (Voss and Gerstein, 2005).
† A volume of 7000 nm3 was estimated to enclose the ribosome (Protein Data Bank ID 4UG0) based on a ~ 2 nm-resolution isosurface calculated using Chimera (Pettersen et al., 2004). Solvent within this isosurface (42%) was treated as bulk vitreous ice for atom number density summations.
‡ Includes solvent atoms.
§ A density of 3.14 g/cm3 was taken for crystalline TCP.