2JUK
guanidino neomycin B recognition of an HIV-1 RNA helix
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H NOESY | 1mM mM HIV-1 frameshift site RNA, 0.5mM mM [U,G,C,A] 100% 15N, 100% 13C HIV-1 frameshift site RNA | 100% D2O | 50 | 6.8 | ambient | 303 | |
2 | 2D 1H-1H TOCSY | 1mM mM HIV-1 frameshift site RNA, 0.5mM mM [U,G,C,A] 100% 15N, 100% 13C HIV-1 frameshift site RNA | 100% D2O | 50 | 6.8 | ambient | 303 | |
3 | 2D HMBC | 1mM mM HIV-1 frameshift site RNA, 0.5mM mM [U,G,C,A] 100% 15N, 100% 13C HIV-1 frameshift site RNA | 100% D2O | 50 | 6.8 | ambient | 303 | |
4 | 2D 1H-13C HSQC | 1mM mM HIV-1 frameshift site RNA, 0.5mM mM [U,G,C,A] 100% 15N, 100% 13C HIV-1 frameshift site RNA | 100% D2O | 50 | 6.8 | ambient | 303 | |
5 | 2D 1H-13C HSQC | 1mM mM HIV-1 frameshift site RNA, 0.5mM mM [U,G,C,A] 100% 15N, 100% 13C HIV-1 frameshift site RNA | 100% D2O | 50 | 6.8 | ambient | 303 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DMX | 750 |
2 | Bruker | DMX | 600 |
3 | Varian | INOVA | 900 |
4 | Varian | INOVA | 800 |
NMR Refinement | ||
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Method | Details | Software |
molecular dynamics | Amber |
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 | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | Amber | Case, D.A. et al. | |
2 | structure solution | CNS | Brunger, A.T. et al. | |
3 | structure visualization | MOLMOL | Koradi, R. et al. | |
4 | chemical shift assignment | Sparky | Goddard, T.D. et al. | |
5 | structure solution | X-PLOR NIH | Schwieters, C.D. et al. | |
6 | collection | XwinNMR | Bruker Biospin | |
7 | collection | NMRPipe | Delaglio, F. et al. |