1P5N
Solution Structure of HCV IRES Domain IIb
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D S-NOESY | 1-2mM HCV IRES domain IIb RNA 10mM phosphate buffer | 96% D2O, 4% H2O | 10mM posphate buffer | 6.40 | ambient | 288 | |
2 | 2D NOESY | 1-2mM HCV IRES domain IIb RNA 10mM phosphate buffer | 100% D2O | 10mM posphate buffer | 6.40 | ambient | 298 | |
3 | DQF-COSY | 1-2mM HCV IRES domain IIb RNA 10mM phosphate buffer | 100% D2O | 10mM posphate buffer | 6.40 | ambient | 298 | |
4 | 2D HP-COSY | 1-2mM HCV IRES domain IIb RNA 10mM phosphate buffer | 100% D2O | 10mM posphate buffer | 6.40 | ambient | 298 | |
5 | 3D_13C-separated_NOESY | 1-2mM HCV IRES domain IIb RNA U-15N,13C 10mM phosphate buffer | 100% D2O | 10mM posphate buffer | 6.40 | ambient | 298 | |
6 | 3D HCP | 1-2mM HCV IRES domain IIb RNA U-15N,13C 10mM phosphate buffer | 100% D2O | 10mM posphate buffer | 6.40 | ambient | 298 | |
7 | 3D HMQC TOCSY | 1-2mM HCV IRES domain IIb RNA U-15N,13C 10mM phosphate buffer | 96% D2O, 4% H2O | 10mM posphate buffer | 6.40 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 500 |
2 | Varian | INOVA | 800 |
NMR Refinement | ||
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Method | Details | Software |
see reference above | see reference above | VNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | lowest restraint violation and total energy |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (minimized average structure) |
Additional NMR Experimental Information | |
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Details | The structure was solved using triple resonance, multidimensional NMR spectroscopy and TROSY-type experiments to measure residual dipolar couplings |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | processing | VNMR | 6.1C | Varian |
2 | data analysis | Sparky | 3 | Goddard, T.D. & Kneller D.G. |
3 | refinement | X-PLOR | 3.1 | Brunger, A.T. |
4 | refinement | CNS | 1.1 | Brunger, A.T. |
5 | refinement | PALES | 1 | Zweckstetter, M. & Bax, A. |