U2/U6 Helix I
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 0.5-0.6 mM RNA | 90% H2O/10% D2O | 15 | 7.0 | ambient | 283 | |
| 2 | 2D 1H-1H NOESY | 0.5-0.6 mM RNA | 100% D2O | 15 | 7.0 | ambient | 298 | |
| 3 | 2D 1H-1H TOCSY | 0.5-0.6 mM RNA | 100% D2O | 15 | 7.0 | ambient | 298 | |
| 4 | 2D 1H-13C HSQC aromatic | 0.5-0.6 mM RNA | 100% D2O | 15 | 7.0 | ambient | 298 | |
| 5 | 2D 1H-13C HSQC aliphatic | 0.5-0.6 mM RNA | 100% D2O | 15 | 7.0 | ambient | 298 | |
| 6 | 2D 1H-15N HMQC | 0.3 mM [U-98% 13C; U-98% 15N] RNA | 90% H2O/10% D2O | 15 | 7.0 | ambient | 283 | |
| 7 | 2D 1H-13C HSQC aromatic | 0.3 mM [U-98% 13C; U-98% 15N] RNA | 100% D2O | 15 | 7.0 | ambient | 298 | |
| 8 | 2D 1H-13C HSQC aliphatic | 0.3 mM [U-98% 13C; U-98% 15N] RNA | 100% D2O | 15 | 7.0 | ambient | 298 | |
| 9 | 2D 1H-15N HMQC | 0.3 mM [U-98% 13C; U-98% 15N] RNA, 17 mg/ml Pf1 phage | 90% H2O/10% D2O | 15 | 7.0 | ambient | 283 | |
| 10 | 2D 1H-13C HSQC aromatic | 0.3 mM [U-98% 13C; U-98% 15N] RNA, 17 mg/ml Pf1 phage | 100% D2O | 15 | 7.0 | ambient | 298 | |
| 11 | 2D 1H-13C HSQC aliphatic | 0.3 mM [U-98% 13C; U-98% 15N] RNA, 17 mg/ml Pf1 phage | 100% D2O | 15 | 7.0 | ambient | 298 | |
| 12 | 2D HNN-COSY | 0.3 mM [U-98% 13C; U-98% 15N] RNA | 90% H2O/10% D2O | 15 | 7.0 | ambient | 283 | |
| 13 | 3D HCCH-TOCSY | 0.3 mM [U-98% 13C; U-98% 15N] RNA | 100% D2O | 15 | 7.0 | ambient | 298 | |
| 14 | 3D HCCH-COSY | 0.3 mM [U-98% 13C; U-98% 15N] RNA | 100% D2O | 15 | 7.0 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DMX | 750 |
| 2 | Varian | INOVA | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | CNS | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 50 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | structure solution | CNS | 1.1 | Brunger, Adams, Clore, Gros, Nilges and Read |
| 2 | collection | XwinNMR | 3.5 | Bruker Biospin |
| 3 | processing | XwinNMR | 3.5 | Bruker Biospin |
| 4 | collection | VnmrJ | 1.1 | Varian |
| 5 | processing | NMRPipe | 97.027.12.56 | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
| 6 | chemical shift assignment | Sparky | 3.114 | Goddard |
| 7 | data analysis | Sparky | 3.114 | Goddard |
| 8 | peak picking | Sparky | 3.114 | Goddard |
| 9 | refinement | X-PLOR NIH | 2.21 | Schwieters, Kuszewski, Tjandra and Clore |