NMR structure of the III-IV-V three-way junction from the VS ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 1D flip-back watergate 1H | 1.5-2.0 mM [U-100% 15N] J345 | 90% H2O/10% D2O | 55 | 6.5 | 288 | ||
| 2 | 2D 1H-15N HSQC | 1.5-2.0 mM [U-100% 15N] J345 | 90% H2O/10% D2O | 55 | 6.5 | 288 | ||
| 3 | 2D 1H-15N HSQC NH2 only | 1.5-2.0 mM [U-100% 15N] J345 | 90% H2O/10% D2O | 55 | 6.5 | 288 | ||
| 4 | 3D 1H-15N NOESY | 1.5-2.0 mM [U-100% 15N] J345 | 90% H2O/10% D2O | 55 | 6.5 | 288 | ||
| 5 | 2D 1H-13C HSQC | 2.0 mM [U-100% 13C; U-100% 15N] J345 | 100% D2O | 55 | 6.5 | 298 | ||
| 6 | 3D 13C-edited HMQC-NOESY | 2.0 mM [U-100% 13C; U-100% 15N] J345 | 100% D2O | 55 | 6.5 | 298 | ||
| 7 | 3D CT-HCCH-COSY | 2.0 mM [U-100% 13C; U-100% 15N] J345 | 100% D2O | 55 | 6.5 | 298 | ||
| 8 | 3D HCCH-TOCSY | 2.0 mM [U-100% 13C; U-100% 15N] J345 | 100% D2O | 55 | 6.5 | 298 | ||
| 9 | 3D 15N-edited NOESY-HSQC | 2.0 mM [U-100% 13C; U-100% 15N] J345 | 90% H2O/10% D2O | 55 | 6.5 | 298 | ||
| 10 | 2D H(NC)-TOCSY-(C)H for guanosine residues | 2.0 mM [U-100% 13C; U-100% 15N] J345 | 90% H2O/10% D2O | 55 | 6.5 | 298 | ||
| 11 | 2D 1H-13C HMQC | 2.0 mM [U-100% 13C; U-100% 15N] J345 | 100% D2O | 55 | 6.5 | 298 | ||
| 12 | 2D 1H-15N MQ-(HC)N(C)H | 2.0 mM [U-100% 13C; U-100% 15N] J345 | 100% D2O | 55 | 6.5 | 298 | ||
| 13 | 2D 1H-15N CPMG-NOESY | 1.5-2.0 mM [U-100% 15N] J345 | 90% H2O/10% D2O | 55 | 6.5 | 288 | ||
| 14 | 2D HNN-COSY | 1.5-2.0 mM [U-100% 15N] J345 | 90% H2O/10% D2O | 55 | 6.5 | 288 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | UNITY | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | NMRDraw | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 300 |
| Conformers Submitted Total Number | 21 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | data analysis | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 2 | processing | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 3 | data analysis | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 4 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 5 | chemical shift assignment | CCPNMR_suite | CCPN | |
| 6 | data analysis | CCPNMR_suite | CCPN | |
| 7 | peak picking | CCPNMR_suite | CCPN | |
| 8 | structure solution | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
| 9 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
