. Author manuscript; available in PMC: 2008 Dec 8.

Published in final edited form as: J Phys Chem B. 2007 May 22;111(23):6577–6585. doi: 10.1021/jp0683871

Table 2.

Statistics for Some Structural Quality Indicators for the SAC Protein^a

Structural Quality Indicators	Final Set of Structures^b	1HY8^c
Residues in Allowed Regions^d (%)	92 ± 1.0	93.8 ± 2.2 ( 95.8 )
Residues in Generously Allowed Regions^e (%)	4.3 ± 0.9	3.4 ± 0.5 ( 2.8 )
Residues in Disallowed Regions ^f (%)	1.5 ± 0.5	2.8 ± 1.0 ( 1.4 )
Number of Abnormally Short Interatomic Distances ^g	22.2 ± 3.8	n/a ( 74 )
Standard Deviation of Omega Values^h (degrees)	5.8° ± 0.3°	n/a ( 0.65° )

^a)

Based on PROCHECK ³⁹ or WHAT_IF. ³⁶ Because we adopted the rigid geometry approximation, i.e., fixed bond lengths and bond angles, departures from values for the idealized covalent geometry are not reported.

^b)

All the values reported in this column were computed from the final nine protein models obtained after step (8), as explained in Results and Discussion section.

^c)

All the values reported in this column, except those from the last two rows, are obtained from Table 1 of Xu et al. ²⁵ The reported standard deviation is based on the averaged values computed for the final ensemble of 22 structures. The values for the minimized average structure (PDB code 1HY8), obtained by averaging the Cartesian coordinates of 22 individual structures of the ensemble, are in parenthesis.

^d)

The reported Residues in Allowed Region are based on a sum of the residues in the ‘most favored regions’ and in the ‘additional allowed regions’, as defined in PROCHECK.³⁹

^e)

By using PROCHECK.³⁹

^f)

By using PROCHECK. ³⁹

^g)

By using WHAT_IF.³⁶ According to Vriend³⁶ “…two atoms have an abnormally short interatomic distance if they are closer than the sum of their van der Waals radii minus 0.4 Angstrom. For hydrogen-bonded pairs, a tolerance of 0.5 Angstrom is used…” The value reported for 1HY8 was computed by using the deposited averaged-minimized structure. n/a means that the corresponding values cannot be reported because the 22 final structures of the ensemble are not available.

^h)

By using WHAT_IF.³⁶ According to Vriend³⁶ “…the omega angles for trans-peptide bonds in a structure are expected to give a Gaussian distribution with the average around 178 degrees and a standard deviation around 5.5 degrees…”. Structures with values for the standard deviation lower than 4° are considered too tightly constrained.³⁶