Solution Structure of the ScYLV P1-P2 Frameshifting Pseudoknot, 20 Lowest Energy Structures
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY | 2mM ScYLV pseudoknot RNA, 100mM KCl, 5mM MgCl2, pH 6.0 | 90% H2O/10% D2O | 100mM KCl; 5mM MgCl2 | 6.0 | ambient | 283 | |
| 2 | 2D NOESY | 2mM ScYLV pseudoknot RNA, 100mM KCl, 5mM MgCl2, pH 6.0 | 100% D2O | 100mM KCl; 5mM MgCl2 | 6.0 | ambient | 298 | |
| 3 | 3D_13C-separated_NOESY | 2mM ScYLV pseudoknot RNA, 100mM KCl, 5mM MgCl2, pH 6.0 | 100% D2O | 100mM KCl; 5mM MgCl2 | 6.0 | ambient | 298 | |
| 4 | CT-TROSY and CT-antiTROSY | 2mM ScYLV pseudoknot RNA, 100mM KCl, 5mM MgCl2, pH 6.0, 12.5mg/ml PF1 phage | 100% D2O | 100mM KCl; 5mM MgCl2 | 6.0 | ambient | 298 | |
| 5 | J-modulated HSQC | 2mM ScYLV pseudoknot RNA, 100mM KCl, 5mM MgCl2, pH 6.0, 12.5mg/ml PF1 phage | 100% D2O | 100mM KCl; 5mM MgCl2 | 6.0 | ambient | 298 | |
| 6 | 2D TOCSY | 2mM ScYLV pseudoknot RNA, 100mM KCl, 5mM MgCl2, pH 6.0 | 100% D2O | 100mM KCl; 5mM MgCl2 | 6.0 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 500 |
| 2 | Varian | INOVA | 600 |
| 3 | Bruker | AVANCE | 900 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | NMRPipe | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 25 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | processing | NMRPipe | 97.027.12.56 | F. Delaglio, S. Grzesiek, G.W. Vuister, G. Zhu, J. Pfeifer and A. Bax |
| 2 | data analysis | Sparky | 3.110 | T. D. Goddard and D. G. Kneller |
| 3 | structure solution | X-PLOR-NIH | 2.9.7 | G.M. Clore , J.Kuszewski, C.D. Schwieters, and N.Tjandra |
| 4 | refinement | X-PLOR-NIH | 2.9.7 | G.M. Clore , J.Kuszewski, C.D. Schwieters, and N.Tjandra |
