Table 1.
Structural Statistics for the Ensemble of 78 Accepted Structures of the PARP-1 F1F2 Dumbbell Complex
| Template Restraints, Protein (Supported by NMR Data; see Experimental Procedures) | |
| Strong NCS (force constant 104 kcal.mol−1) to 3ODA | F1, res. 9–36, 49–59, and 66–89 (all atoms) |
| Weak NCS (force constant 50 kcal.mol−1) to 3ODA | F1, res. 6–8, 37–48, 60–65, and 90–91 (N, Cα, C′), res. 44 (all carbons) |
| Strong NCS (force constant 104 kcal.mol−1) to 3ODC | F2, res. 114–140 and 155–199 (all atoms) |
| Weak NCS (force constant 50 kcal.mol−1) to 3ODC | F2, res. 109–113, 141–154, and 200–201 (N, Cα, C′) |
| Template Restraints, DNA (Supported by NMR Data; see Experimental Procedures) | |
| Distance (O3′, O5′, intra- and inter-strand) | stem 1, 48; stem 2, 48 |
| Dihedral angle | stem 1, 193; stem 2, 168 |
| tetraloops, 95 | |
| Base pair H-bond distance |
stem 1, 24 (6 GC, 3 AT base pairs) |
| stem 2, 25 (7 GC, 2 AT base pairs) | |
| tetraloops, 6 (2 base pairs) | |
| NMR-Derived Restraints on Domain Interactions and Orientation | |
| Interdomain NOE-derived distances | 6 (from 15 NOEs; Table S2) |
| Intermolecular NOE-derived distances | 12 (from 17 NOEs; Table S2) |
| RDCs (NH) | |
| F1 | 42 |
| F2 | 43 |
| XPLOR-NIH Energy Terms (kcal.mol−1) | |
| E(total) | 4159 ± 714 |
| E(tensor) | 1123 ± 4.0 |
| E(distance) | 0.70 ± 0.39 |
| E(NCS) | 268 ± 8 |
| E(VDW) | 973 ± 499 |
| Violations | |
| NOE (max, mean ± SD) | 0.177 Å, 0.046 ± 0.035 Å |
| QRDC (mean ± SD) | 24.47% ± 0.04% |
| Deviations from Ideal Geometry (RMSD) | |
| Bonds | 0.0042 Å |
| Angles | 0.780° |
| Impropers | 0.656° |
| Protein Ramachandran Statistics | |
| Residues 6–91, 109–201 | F1: 91.7%, 7.5%, 0.8%, 0.0% |
| (core, allowed, generously allowed, disallowed) | F2: 87.0%, 13.0%, 0.0%, 0.0% |
| Co-ordinate Precision (Mean RMSD to Mean Structure)b | |
| F1, F2, whole DNA (all heavy) | 0.524 ± 0.172 Å |
| F1, F2, whole DNA (backbone) | 0.352 ± 0.205 Å |
| F1, F2, DNA stem 1, DNA stem 2 (backbone) | 0.340 ± 0.211 Å |
| F1, DNA stem1 (backbone) | 0.036 ± 0.027 Å |
| F2, DNA stem 2 (backbone) | 0.042 ± 0.025 Å |
Abbreviations: res, residues; VDW, van der Waals; RMSD, root-mean-square deviation. For further details, see Supplemental Experimental Procedures. aPrior to addition of disordered protein residues 1–5, 92–108, and 202–214.
b
F1, residues 6–91; F2, residues 109–201; DNA stem 1, nt 1–22; DNA stem 2, nt 24–45 (excluding C24 O5′ and P).