. 2011 Aug 5;411(1):286–297. doi: 10.1016/j.jmb.2011.05.033

Table 1.

Refinement details for the SH3 domain (PDB ID: 1H8K), villin headpiece (PDB ID: 2RJY), and ubiquitin (PDB ID: 3EFU)

	PDB ID 1H8K				PDB ID 2RJY				PDB ID 3EFU
	unrestr₀	unrestr	restr	restr_or	unrestr₀	unrestr	restr	restr_or	unrestr₀	unrestr	restr	restr_or
R	0.237	0.233	0.248	0.245	0.202	0.202	0.205	0.206	0.210	0.226	0.250	0.245
R_free	0.324	0.360	0.324	0.312	0.227	0.227	0.232	0.231	0.308	0.318	0.338	0.334
RMS (Å)	0.104	0.150	0.111	0.106	0.116	0.116	0.119	0.116	0.130	0.187	0.164	0.147
Distance match (%)	13.8	19.7	59.0	7.5	20.0	22.1	44.5	13.4	18.3	25.7	46.6	9.4
RMS bond length (Å)	0.012	0.017	0.013	0.015	0.027	0.028	0.027	0.026	0.148	0.070	0.072	0.070
RMS bond angle (°)	1.395	1.789	1.459	1.529	2.200	2.278	2.198	2.131	1.926	1.560	1.710	1.946
RMS chiral volume (Å³)	0.091	0.120	0.104	0.102	0.143	0.148	0.138	0.136	0.133	0.096	0.095	0.114

RMSD is calculated between the interatomic distances used as restraints in the refinement and the distances in each of the models, as well as for the following stereochemical quantities: bond lengths, bond angles, and chiral volumes. Distance match for each model represents the percentage of interatomic distances closest to the calculated restraints compared to the distances in the other two models. The following labels apply: unrestr₀—structure refined without external restraints; unrestr—structure refined from unrestr₀ without external restraints; restr—structure refined from unrestr₀ using corrections calculated according to Busing–Levy equations as restraints; restr_or—structure refined from unrestr₀ using distances without any corrections as restraints.