Table 1.
Structural statistics for the 20 structures of RAPd1T
| Parameter | Value |
|---|---|
| Distance restraints (all) | 1178 |
| Intraresidue | 218 |
| Sequential (|i − j| = 1) | 296 |
| Medium range (1 < |i − j|24) | 363 |
| Long range (|i − j| > 4) | 301 |
| Hydrogen bonds | 41 |
| Dihedral angle restraints (all) | 95 |
| φ | 54 |
| χ | 41 |
| Deviations from experimentally derived restraint | |
| Distance restraints | |
| No. of violations in the interval | |
| 0.1–0.2 Å | 16.5 |
| 0.2–0.3 Å | 1.7 |
| 0.3–0.4 Å | 0.1 |
| Hydrogen bonds > 0.2 Å | 0 |
| rmsd, Å | 0.023 ± 0.001 |
| Deviations from dihedral angle restraints, ° | |
| No. of violations larger than 3 | 0 |
| rmsd | 0.12 ± 0.06 |
| Deviations from idealized geometry | |
| Impropers, ° | |
| >5 | 0 |
| rmsd | 0.49 ± 0.01 |
| Bonds, Å | |
| >0.05 | 0 |
| rmsd | 0.0027 ± 0.001 |
| Angles, ° | |
| >5 | 0.1 |
| rmsd | 0.58 ± 0.01 |
| Energies, kcal·mol−1* | |
| NOE | 32.1 ± 3.8 |
| Dihedral angle restraint | 0.097 ± 0.081 |
| Bond | 9.94 ± 0.96 |
| Angle | 130.2 ± 5.8 |
| Improper | 25.2 ± 1.2 |
| Repel | 26.5 ± 3.8 |
| van der Waals | −145.0 ± 15.3 |
| Hydrogen bond restraint | 8.98 ± 0.67 |
| Hydrogen bond | −69.1 ± 3.5 |
| Pairwise rmsd of atomic positions, ņ | |
| Backbone (N, Cα, C) | |
| residues 18–91 | 0.48 ± 0.08 |
| All heavy atoms | |
| residues 18–91 | 1.22 ± 0.11 |
The number of experimentally derived restraints used in the structure calculations, and average values per structure of the deviations between the 20 accepted structures, and the experimental restraints or idealized geometry are shown.
Energies were calculated using the final force constants of: kNOE = 50 kcal·mol−1·Å−2, kcdih = 200 kcal·mol−1·rad−2, kbond = 1,000 kcal·mol −1·Å−2, kangle = 500 kcal·mol−1·rad−2, kimproper = 500 kcal·mol−1·Å −2, krepel = 4.0 kcal·mol−1·Å−2, and with the final van der Waals hard sphere radius set to 0.75 of the values calculated from the x-plor parallhdg_new.pro parameter file. The van der Waals energy and hydrogen bond energies were calculated using the x-plor switched Lennard-Jones van der Waals energy function and hydrogen bond function using the parmallh3x.pro parameter file, but they were not included in the target functions used in the simulated annealing procedure.
The pairwise rmsds between the 20 reported structures are also listed.