2M5U
NMR structure of the P4 hairpin of the CPEB3 ribozyme
SOLUTION NMR
NMR Experiment | ||||||||
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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 | |||
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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 | |
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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 |