Table 2. Stereochemical and energetic analysis of yGPN comparative models.
| Score | PAB0955 | yGPN1 | yGPN2 | yGPN3 |
|---|---|---|---|---|
| PROSA |
-9.32 |
-6.37 |
-6.96 |
-7.44 |
| HBOND |
398 |
383 |
366 |
353 |
| PROCHECK |
91.7 |
90.5 |
89.2 |
93.5 |
| DDFIRE |
-669.1 |
-604.9 |
-613.7 |
-598.9 |
| FRST |
-33162.4 |
-11619.5 |
-14911.3 |
-18082.2 |
| XPLOR |
-447.3 |
-459.6 |
-351.7 |
-570.9 |
| MOLPROBITY |
2.42 (52nd percentile) |
2.28 (60th percentile) |
2.44 (50th percentile) |
2.21 (64th percentile) |
| Cα-RMSD | 0.0 | 0.141 (241) | 0.173 (236) | 0.186 (236) |
Values for PROSA are Z-scores obtained from the Prosa2000 package38 (lower values indicate better structures).
Values for HBOND show the total number of detected hydrogen bonds using heavy atoms of the structures (in-house tool, higher values indicate better structures).
Values for PROCHECK indicate the percentage of dihedral angle (φ,ψ) values located within the most favored regions37 (higher values indicate better structures).
Values for DDFIRE are obtained from the DFIRE-pseudo potential function54 in units of kcal/mol (lower values indicate better structures).
Values for FRST are obtained from the pseudo-potential energy FRST40 in pseudo units (lower values indicate better structures).
Values for XPLOR are those from the non-bonded van der Waals potential energy terms using Charmm22 force field44 in unit of kcal/mol (lower values indicate better structures).
Values for MolProbity were obtained from the web server.55 The lower the score, the better the structure quality; 100th percentile represents an ideal protein structure whereas 0th percentile represents the worst case.
Values for Cα-RMSD obtained from the sup3d global superposition20 indicate the RMSD between Cα atoms of the PAB0955 template and Cα atoms from each model. The number of parenthesis indicated the number of superimposed residues that have their Cα-RMSDs below the given value. The total alignment length is 274 residues.