1ESY
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 | ||||||||
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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 | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DMX | 600 |
2 | Bruker | DRX | 800 |
NMR Refinement | ||
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Method | Details | Software |
Distance Geometry, Simulated annealing, Energy mimimization | XwinNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | target function |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (fewest violations) |
Additional NMR Experimental Information | |
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Details | experimental temperature set to either 298 or 278 |
Computation: NMR Software | ||||
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# | 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. |