International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

International Tables for Crystallography (2006). Vol. F, ch. 22.1, p. 536   | 1 | 2 |

Table 22.1.1.1 

M. Gersteina* and F. M. Richardsa

Table 22.1.1.1| top | pdf |
Standard atomic radii (Å)

For `*' see following notes on specific sets of values. Bondi: Values assigned on the basis of observed packing in condensed phases (Bondi, 1968[link]). Lee & Richards: Values adapted from Bondi (1964)[link] and used in Lee & Richards (1971)[link]. Shrake & Rupley: Values taken from Pauling (1960)[link] and used in Shrake & Rupley (1973)[link]. >C= value can be either 1.5 or 1.85. Richards: Minor modification of the original Bondi set in Richards (1974)[link]. (Rationale not given.) See original paper for discussion of aromatic carbon value. Chothia: From packing in amino-acid crystal structures. Used in Chothia (1975)[link]. Richmond & Richards: No rationale given for values used in Richmond & Richards (1978)[link]. Gelin & Karplus: Origin of values not specified. Used in Gelin & Karplus (1979)[link]. Dunfield et al.: Detailed description of deconvolution of molecular crystal energies. Values represent one-half of the heavy-atom separation at the minimum of the Lennard–Jones 6–12 potential functions for symmetrical interactions. Used in Nemethy et al. (1983)[link] and Dunfield et al. (1979)[link]. ENCAD: A set of radii, derived in Gerstein et al. (1995)[link], based solely on the ENCAD molecular dynamics potential function in Levitt et al. (1995)[link]. To determine these radii, the separation at which the 6–12 Lennard–Jones interaction energy between equivalent atoms was 0.25 [k_{B}T] was determined (0.15 kcal mol−1; 1 kcal = 4.184 kJ). CHARMM: Determined in the same way as the ENCAD set, but for the CHARMM potential (Brooks et al., 1983[link]) (parameter set 19). Tsai et al.: Values derived from a new analysis (Tsai et al., 1999[link]) of the most common distances of approach of atoms in the Cambridge Structural Database.

Atom type and symbolBondi (1968)[link]Lee & Richards (1971)[link]Shrake & Rupley (1973)[link]Richards (1974)[link]Chothia (1975)[link]Richmond & Richards (1978)[link]Gelin & Karplus (1979)[link]Dunfield et al. (1979)[link]ENCAD derived (1995)CHARMM derived (1995)Tsai et al. (1999)[link]
[-\hbox{CH}_{3}] Aliphatic, methyl 2.00 1.80 2.00 2.00 1.87 1.90 1.95 2.13 1.82 1.88 1.88
[-\hbox{CH}_{2}-] Aliphatic, methyl 2.00 1.80 2.00 2.00 1.87 1.90 1.90 2.23 1.82 1.88 1.88
[\gt\!\hbox{CH}-] Aliphatic, CH 1.70 2.00 2.00 1.87 1.90 1.85 2.38 1.82 1.88 1.88
>=[\hbox{CH}\!=] Aromatic, CH 1.80 1.85 * 1.76 1.70 1.90 2.10 1.74 1.80 1.76
[\gt\!\hbox{C}\!=] Trigonal, aromatic 1.74 1.80 * 1.70 1.76 1.70 1.80 1.85 1.74 1.80 1.61
[-\hbox{NH}_{3}^{+}] Amino, protonated 1.80 1.50 2.00 1.50 0.70 1.75 1.68 1.40 1.64
[-\hbox{NH}_{2}] Amino or amide 1.75 1.80 1.50 1.65 1.70 1.70 1.68 1.40 1.64
[\gt\!\hbox{NH}] Peptide, NH or N 1.65 1.52 1.40 1.70 1.65 1.70 1.65 1.75 1.68 1.40 1.64
[=\!\hbox{O}] Carbonyl oxygen 1.50 1.80 1.40 1.40 1.40 1.40 1.60 1.56 1.34 1.38 1.42
[-\hbox{OH}] Alcoholic hydroxyl 1.80 1.40 1.60 1.40 1.40 1.70 1.54 1.53 1.46
[-\hbox{OM}] Carboxyl oxygen 1.80 1.89 1.50 1.40 1.40 1.60 1.62 1.34 1.41 1.42
[-\hbox{SH}] Sulfhydryl 1.80 1.85 1.85 1.80 1.90 1.82 1.56 1.77
[-\hbox{S}-] Thioether or –S–S– 1.80 1.80 1.85 1.80 1.90 2.08 1.82 1.56 1.77