2OJ8
NMR structure of the UGUU tetraloop of Duck Epsilon apical stem loop of the Hepatitis B virus
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 1.2 mM RNA, 10mM Na phosphate buffer, pH 6.7, 0.1 mM EDTA, 95% H2O, 5% D2O | 10mM | 6.7 | ambient | 5 | ||
2 | 2D NOESY | 1.2 mM RNA, 10mM Na phosphate buffer, pH 6.7, 0.1 mM EDTA, 95% H2O, 5% D2O | 10mM | 6.7 | ambient | 15 | ||
3 | HMQC-15N/1H | 1.0 mM 13C/15N/2H-U labeled RNA, 10mM Na phosphate buffer, pH 6.7, 0.1 mM EDTA, 95% H2O, 5% D2O | 10mM | 6.7 | ambient | 5 | ||
4 | DQF-COSY | 1.2 mM RNA, 10mM Na phosphate buffer, pH 6.7, 0.1 mM EDTA, D2O | 10mM | 6.7 | ambient | 25 | ||
5 | HMQC-13C/1H | 1.0 mM 13C/15N/2H-U labeled RNA, 10mM Na phosphate buffer, pH 6.7, 0.1 mM EDTA, D2O | 10mM | 6.7 | ambient | 25 | ||
6 | 2D NOESY | 1.2 mM RNA, 10mM Na phosphate buffer, pH 6.7, 0.1 mM EDTA, D2O | 10mM | 6.7 | ambient | 25 |
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 |
Torsion angle dynamics with chemical shift refinement using XPLOR 8.351 with home written refinement chemical shift refinement module | X-PLOR |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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Details | In addition TOCSY spectra and 31P 1D and 31P HMBC spectra were recorded |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | X-PLOR | 3.851* | Girard, F.C., Ottink O.M., Ampt, K.A.M., Tessari, M., Wijmenga, S.S. |