2M5U
NMR structure of the P4 hairpin of the CPEB3 ribozyme
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 0.7-0.8 mM RNA (natural abundance) | 10% D2O/90% H2O | 50 | 6.8 | ambient | 298 | |
| 2 | 2D 1H-1H NOESY | 0.7-0.8 mM RNA (natural abundance) | 10% D2O/90% H2O | 50 | 6.8 | ambient | 298 | |
| 3 | 2D 1H-1H TOCSY | 0.7-0.8 mM RNA (natural abundance) | 10% D2O/90% H2O | 50 | 6.8 | ambient | 298 | |
| 4 | 2D 1H-1H NOESY | 0.7-0.8 mM RNA (natural abundance) | 100% D2O | 50 | 6.8 | ambient | 298 | |
| 5 | 2D 1H-1H NOESY | 0.7-0.8 mM RNA (natural abundance) | 100% D2O | 50 | 6.8 | ambient | 298 | |
| 6 | 1D 31P | 0.7-0.8 mM RNA (natural abundance) | 10% D2O/90% H2O | 50 | 6.8 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 700 |
| 2 | Bruker | AVANCE | 600 |
| 3 | Bruker | AVANCE | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| molecular dynamics | DYANA | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 150 |
| Conformers Submitted Total Number | 15 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | structure solution | DYANA | 1.5 | Guntert, Braun and Wuthrich |
| 2 | structure solution | CNS | 1.2 | Brunger, Adams, Clore, Gros, Nilges and Read |
| 3 | refinement | X-PLOR NIH | 2.3 | Schwieters, Kuszewski, Tjandra and Clore |
| 4 | data analysis | TopSpin | 3.0 | Bruker Biospin |
| 5 | peak picking | Sparky | Goddard | |
| 6 | collection | TopSpin | 3.0 | Bruker Biospin |
| 7 | processing | TopSpin | 3.0 | Bruker Biospin |
