1S34
Solution structure of residues 907-929 from Rous Sarcoma Virus
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY | 1 mM 23 mer RNA (NRS23) | >99% D2O | 25mM NaCl, 10 mM Sodium Phosphate | 6.5 | ambient | 298 | |
| 2 | 3D_13C-separated_NOESY | 1 mM 23 mer RNA (NRS23) | >99% D2O | 25mM NaCl, 10 mM Sodium Phosphate | 6.5 | ambient | 298 | |
| 3 | DQF-COSY | 1 mM 23 mer RNA (NRS23) | >99% D2O | 25mM NaCl, 10 mM Sodium Phosphate | 6.5 | ambient | 298 | |
| 4 | HNN-COSY | 1 mM 23 mer RNA (NRS23) | >99% D2O | 25mM NaCl, 10 mM Sodium Phosphate | 6.5 | ambient | 298 | |
| 5 | 2D NOESY | 1 mM NRS23 | 90% H2O/10% D2O | 25mM NaCl, 10 mM Sodium Phosphate | 6.5 | ambient | 288 | |
| 6 | HCP | 1 mM 23 mer RNA (NRS23) | >99% D2O | 25mM NaCl, 10 mM Sodium Phosphate | 6.5 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DRX | 500 |
| 2 | Varian | INOVA | 500 |
| 3 | Varian | INOVA | 600 |
| 4 | Varian | INOVA | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| Simulated annealing. Refinement using torsion angle dynamics and the DELPHIC database | DELPHIC torsion angle potential was used for the whole molecule. The base position potential was excluded for residues 913, and 917 to 920. Protocol from Clore and Kuszewski (J Am Chem Soc. 2003. 125(6):1518-25) | VNMR |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 15 |
| Representative Model | 1 (lowest energy) |
| Additional NMR Experimental Information | |
|---|---|
| Details | RDC restraints were obtained for the base one bond H-C and H-N using HSQC experiments. RDC restraints for the ribose were obtained from measurements on an Relay HCCH-COSY (Vallurupalli and Moore, J Biomol NMR. 2002. 24(1):63-6). Anisotropic conditions were ~20 mg/ml pf1 phage. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | VNMR | 6.1 | varian |
| 2 | processing | NMRPipe | 4.1 | F. Delaglio, S. Grzesiek, G. Vuister, G. Zhu, J. Pfeifer, and A. Bax |
| 3 | data analysis | NMRDraw | 4.1 | Delaglio, F. |
| 4 | data analysis | NMRView | 5.0.4 | Johnson and Blevins |
| 5 | structure solution | X-PLOR | NIH 2.0.6 | C.D. Schwieters, J.J. Kuszewski, N. Tjandra, and G.M. Clore |
| 6 | refinement | X-PLOR | NIH 2.0.6 | C.D. Schwieters, J.J. Kuszewski, N. Tjandra, and G.M. Clore |
