1PJY
Solution structure of the HIV-1 frameshift inducing stem-loop RNA
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 1 mM HIV-1 frameshift inducing stem-loop RNA | 90% H2O/10% D2O, or 99.99% D2O | 50 mM | 6.8 | ambient | 303 | |
2 | 2D TOCSY | 1 mM HIV-1 frameshift inducing stem-loop RNA | 90% H2O/10% D2O, or 99.99% D2O | 50 mM | 6.8 | ambient | 303 | |
3 | 3D_13C-separated_NOESY | 1 mM HIV-1 frameshift inducing stem-loop RNA | 90% H2O/10% D2O, or 99.99% D2O | 50 mM | 6.8 | ambient | 303 | |
4 | 2D HNN-COSY | 1 mM HIV-1 frameshift inducing stem-loop RNA | 90% H2O/10% D2O, or 99.99% D2O | 50 mM | 6.8 | ambient | 298 | |
5 | 2D NOESY | 1 mM HIV-1 frameshift inducing stem-loop RNA | 90% H2O/10% D2O, or 99.99% D2O | 50 mM | 6.8 | ambient | 283 | |
6 | 2D 1H-13C HSQC | 1 mM HIV-1 frameshift inducing stem-loop RNA | 90% H2O/10% D2O, or 99.99% D2O | 50 mM | 6.8 | ambient | 303 |
NMR Refinement | ||
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Method | Details | Software |
torsion angle molecular dynamics, Cartesian space simulated annealing and molecular dynamics, residual dipolar coupling | XwinNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | Submitted confermers represent the 20 lowest energy structures with no NOE violations greater than 0.2 Angstroms and no dihedral violations greater than 5 degrees |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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Details | The incorporation of residual dipolar couplings and the direct detection of hydrogen bonds with HNN-COSY were used in solving this structure |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | XwinNMR | 2.6 | |
2 | refinement | CNS | 1.1 | Brunger |
3 | processing | Felix | 98 | |
4 | data analysis | Sparky | 3.72 |