NMR STRUCTURE OF STEM LOOP SL2 OF THE HIV-1 PSI RNA PACKAGING SIGNAL REVEALS A NOVEL A-U-A BASE-TRIPLE PLATFORM
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY | 0.6-1.2 mM SL2 RNA, Natural abundance, 25 mM Na-d3-acetate buffer | 100% D2O | 25 mM NaCl | 5.5 | ambient | 298 | |
| 2 | DQF-COSY | 0.6-1.2 mM SL2 RNA, Natural abundance, 25 mM Na-d3-acetate buffer | 100% D2O | 25 mM NaCl | 5.5 | ambient | 298 | |
| 3 | 2D NOESY | 0.6-1.2 mM SL2 RNA, Natural abundance, 25 mM Na-d3-acetate buffer | 90% H2O/10% D2O | |||||
| 4 | 3D_13C-separated_NOESY | 0.6-1.2 mM SL2 RNA, Natural abundance, 25 mM Na-d3-acetate buffer | 100% D2O | |||||
| 5 | 3D_13C-separated_ROESY | 0.6-1.2 mM SL2 RNA, Natural abundance, 25 mM Na-d3-acetate buffer | 100% D2O | |||||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DMX | 600 |
| 2 | Bruker | DRX | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| Distance Geometry, Simulated annealing, Energy mimimization | XwinNMR | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | target function |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (fewest violations) |
| Additional NMR Experimental Information | |
|---|---|
| Details | experimental temperature set to either 298 or 278 |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | XwinNMR | 2.6 | Brucker |
| 2 | processing | NMRPipe | 1.0 | Delaglio, Gresiek, Vuister, Zhu, and Bax |
| 3 | data analysis | NMRView | 3.0 | Johnson, and Blevins |
| 4 | structure solution | DYANA | 1.5 | Guntert and Mumenthaler |
| 5 | refinement | CNS | 1.0 | Brunger et al. |
