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. 2017 Nov 6;6:e29929. doi: 10.7554/eLife.29929

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.