2JTP
Solution Structure of the Frameshift-Inducing RNA Stem-Loop in SIV
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H TOCSY | 1 mM SIV17-50 RNA (34-MER) | 100% D2O | 7.0 | ambient | 308 | ||
| 2 | 2D 1H-1H NOESY | 1 mM SIV17-50 RNA (34-MER) | 100% D2O | 7.0 | ambient | 308 | ||
| 3 | 2D 1H-1H COSY | 1 mM SIV17-50 RNA (34-MER) | 90% H2O/10% D2O | 7.0 | ambient | 308 | ||
| 4 | 2D 1H-15N HSQC | 1 mM [U-100% 13C; U-100% 15N] SIV17-50 RNA (34-MER) | 100% D2O | 7.0 | ambient | 308 | ||
| 5 | 2D 1H-13C HSQC | 1 mM [U-100% 13C; U-100% 15N] SIV17-50 RNA (34-MER) | 100% D2O | 7.0 | ambient | 308 | ||
| 6 | 3D 1H-13C-1H HCCH-TOCSY | 1 mM [U-100% 13C; U-100% 15N] SIV17-50 RNA (34-MER) | 100% D2O | 7.0 | ambient | 308 | ||
| 7 | 3D NOESY-HMQC | 1 mM [U-100% 13C; U-100% 15N] SIV17-50 RNA (34-MER) | 100% D2O | 7.0 | ambient | 308 | ||
| 8 | J-MODULATED 1H-13C CT-HSQC | 1 mM [U-100% 13C; U-100% 15N] SIV17-50 RNA (34-MER) | 90% H2O/10% D2O | 7.0 | ambient | 308 | ||
| 9 | J-MODULATED 1H-13C CT-HSQC | 1 mM [U-100% 13C; U-100% 15N] SIV17-50 RNA (34-MER) | 90% H2O/10% D2O | 7.0 | ambient | 308 | ||
| 10 | 2D 1H-1H NOESY | 1 mM SIV17-50 RNA (34-MER) | 90% H2O/10% D2O | 7.0 | ambient | 308 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DMX | 750 |
| 2 | Bruker | DMX | 600 |
| 3 | Varian | INOVA | 600 |
| 4 | Varian | INOVA | 800 |
| 5 | Bruker | DMX | 500 |
| 6 | Varian | INOVA | 900 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing, torsion angle dynamics, molecular dynamics, residual dipolar couplings | XwinNMR | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | XwinNMR | 3.5 | Bruker Biospin |
| 2 | processing | XwinNMR | 3.5 | Bruker Biospin |
| 3 | peak picking | Sparky | 3.111 | Goddard |
| 4 | data analysis | Sparky | 3.111 | Goddard |
| 5 | structure solution | CNS | 1.1 | Brunger, Adams, Clore, Gros, Nilges and Read |
| 6 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
| 7 | structure solution | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
| 8 | collection | VNMR | Varian | |
| 9 | processing | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 10 | peak picking | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 11 | data analysis | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
