Skip to main content

Advertisement

Table 2 Quality of the model. A: Parameters reflecting the quality of the model checked by «WHAT IF» [29]. B: Quality of chain of the model. The model is verified at 2Å resolution. Parameter values in the table represent observed values for the GBV-C polymerase model compared with typical values obtained for well refined structures at the same resolution [28].

From: The modeled structure of the RNA dependent RNA polymerase of GBV-C Virus suggests a role for motif E in Flaviviridae RNA polymerases

A
Structure Z-scores:
   1st generation packing quality -1.577     
   2nd generation packing quality -2.94     
   Ramachandran plot appearance -0.74     
   chi-1/chi-2 rotamer normality -0.224     
   Backbone conformation -0.904     
RMS Z-scores, should be close to 1.0:
   Bond lengths 0.950     
   Bond angles 1.426     
   Omega angle restraints -0.923     
   Inside/Outside distribution 1.096     
B
Stereochemical parameter N° of data points Parameter valueTypical valueBand width N° of bandwidth
Stereochemistry of main-chain
   Percentage residues in A, B, L 438 89 83.8 10 0.5
   Omega angle S.D 507 6.8 6 3 0.3
   Bad contacts 100 residues 3 0.6 4.2 10 -0.4
   Zeta angle S.D. 476 2.8 3.1 1.6 -0.2
   Hydrogen bond energy S.D. 305 0.7 0.8 0.2 -0.4
Stereochemistry of side-chain
   Chi-1 gauche minus S.D. 79 15.7 18.1 6.5 -0.4
   Chi-1 trans S.D. 103 13.2 19 5.3 -1.1
   Chi-1 gauche plus S.D. 205 11.4 17.5 4.9 -1.2
   Chi-1 pooled S.D. 387 13 18.2 4.8 -1.1
   Chi-2 trans S.D. 114 15.7 20.4 5 -0.9