1TJZ
Solution Structure of the Active Site Stem-Loop of the VS Ribozyme
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 1 mM VSVI RNA, 90% H2O, 10% D2O | 90% H2O/10% D2O | 6.0 | ambient | 283 | ||
2 | 2D NOESY | 1 mM VSVI RNA, 90% H2O, 10% D2O | 100% D2O | 6.0 | ambient | 293 | ||
3 | DQF-COSY | 1 mM VSVI RNA, 90% H2O, 10% D2O | 100% D2O | 6.0 | ambient | 293 | ||
4 | 2D TOCSY | 1 mM VSVI RNA, 90% H2O, 10% D2O | 100% D2O | 6.0 | ambient | 293 | ||
5 | 3D_13C-separated_NOESY | 1 mM VSVI RNA U-15N,13C | 100% D2O | 6.0 | ambient | 293 | ||
6 | 2D NOESY | 1 mM VSVI RNA | 100% D2O | 6.0 | ambient | 293 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DRX | 600 |
NMR Refinement | ||
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Method | Details | Software |
The structure calculations utilized standard simulated annealing protocols. | The final structures are based on a total of 699 restraints: 582 NOE-derived restraints, 52 dihedral angle restraints, 9 planarity restraints, and 56 distance restraints from hydrogen bonds. | XwinNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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Details | The structure was determined from restraints derived from homo- and heteronuclear experiments. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | XwinNMR | 3.5 | |
2 | data analysis | Sparky | 3.106 | |
3 | structure solution | CNS | 1.1 | |
4 | processing | XwinNMR | 3.5 | |
5 | refinement | CNS | 1.1 |