Space Constrained Homology Modelling: The Paradigm of the RNA-Dependent RNA Polymerase of Dengue (Type II) Virus

Table 1

Parameters reflecting the quality of the Dengue polymerase model calculated by PROCHECK [25]. Parameter values represent observed values for the Dengue polymerase model produced by the cavity space-aided approach compared to typical values obtained refined structures at 2.9 Å.

Stereochemical parameters	Number of data points	Parameter value	Typical value	Band width	Number of band widths from mean	Quality compared to structures at 2.9 Å
A: main chain parameters
Percentage residues in A, B, L	490	71.0	68.7	10.0	0.	Inside
Omega angle st dev	545	9.0	6.0	3.0	1.0	Inside
Bad contacts/100 residues	0	0.0	17.9	10.0	−1.8	BETTER
Zeta angle st dev	508	3.3	3.1	1.6	0.1	Inside
H-bond energy st dev	290	0.7	1.0	0.2	−1.7	BETTER
Overall G-factor	547	−1.0	−0.8	0.3	−0.9	Inside
B: side chain parameters
Chi-1 gauche minus st dev	86	11.5	26.3	6.5	−2.3	BETTER
Chi-1 trans st dev	168	11.3	25.7	5.3	−2.7	BETTER
Chi-1 gauche plus st dev	203	12.1	24.3	4.9	−2.5	BETTER
Chi-1 pooled st dev	457	12.9	25.1	4.8	−2.5	BETTER
Chi-2 trans st dev	109	13.5	25.3	5.0	−2.3	BETTER