2JTP
Solution Structure of the Frameshift-Inducing RNA Stem-Loop in SIV
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H TOCSY | 1 mM SIV17-50 RNA (34-MER) | 100% D2O | 7.0 | ambient | 308 | ||
2 | 2D 1H-1H NOESY | 1 mM SIV17-50 RNA (34-MER) | 100% D2O | 7.0 | ambient | 308 | ||
3 | 2D 1H-1H COSY | 1 mM SIV17-50 RNA (34-MER) | 90% H2O/10% D2O | 7.0 | ambient | 308 | ||
4 | 2D 1H-15N HSQC | 1 mM [U-100% 13C; U-100% 15N] SIV17-50 RNA (34-MER) | 100% D2O | 7.0 | ambient | 308 | ||
5 | 2D 1H-13C HSQC | 1 mM [U-100% 13C; U-100% 15N] SIV17-50 RNA (34-MER) | 100% D2O | 7.0 | ambient | 308 | ||
6 | 3D 1H-13C-1H HCCH-TOCSY | 1 mM [U-100% 13C; U-100% 15N] SIV17-50 RNA (34-MER) | 100% D2O | 7.0 | ambient | 308 | ||
7 | 3D NOESY-HMQC | 1 mM [U-100% 13C; U-100% 15N] SIV17-50 RNA (34-MER) | 100% D2O | 7.0 | ambient | 308 | ||
8 | J-MODULATED 1H-13C CT-HSQC | 1 mM [U-100% 13C; U-100% 15N] SIV17-50 RNA (34-MER) | 90% H2O/10% D2O | 7.0 | ambient | 308 | ||
9 | J-MODULATED 1H-13C CT-HSQC | 1 mM [U-100% 13C; U-100% 15N] SIV17-50 RNA (34-MER) | 90% H2O/10% D2O | 7.0 | ambient | 308 | ||
10 | 2D 1H-1H NOESY | 1 mM SIV17-50 RNA (34-MER) | 90% H2O/10% D2O | 7.0 | ambient | 308 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DMX | 750 |
2 | Bruker | DMX | 600 |
3 | Varian | INOVA | 600 |
4 | Varian | INOVA | 800 |
5 | Bruker | DMX | 500 |
6 | Varian | INOVA | 900 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing, torsion angle dynamics, molecular dynamics, residual dipolar couplings | 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) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | collection | XwinNMR | 3.5 | Bruker Biospin |
2 | processing | XwinNMR | 3.5 | Bruker Biospin |
3 | peak picking | Sparky | 3.111 | Goddard |
4 | data analysis | Sparky | 3.111 | Goddard |
5 | structure solution | CNS | 1.1 | Brunger, Adams, Clore, Gros, Nilges and Read |
6 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
7 | structure solution | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
8 | collection | VNMR | Varian | |
9 | processing | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
10 | peak picking | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
11 | data analysis | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |