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].
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 |