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Quadruplex structure of an RNA aptamer against bovine prion protein
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 1mM RNA-1, 10mM potassium phosphate-2, 100mM potassium chloride-3, 0.01mM DSS-4, 3mM sodium azide-5 95% H2O/5% D2O 0.1 6.2 ambient atm 278 2 2D 1H-1H NOESY 1mM RNA-1, 10mM potassium phosphate-2, 100mM potassium chloride-3, 0.01mM DSS-4, 3mM sodium azide-5 95% H2O/5% D2O 0.1 6.2 ambient atm 303 3 2D 1H-1H NOESY 1mM RNA-6, 10mM potassium phosphate-7, 100mM potassium chloride-8, 0.01mM DSS-9, 3mM sodium azide-10, 95% H2O/5% D2O 100% D2O 0.1 6.2 ambient atm 303 4 2D 1H-1H TOCSY 1mM RNA-1, 10mM potassium phosphate-2, 100mM potassium chloride-3, 0.01mM DSS-4, 3mM sodium azide-5 95% H2O/5% D2O 0.1 6.2 ambient atm 303 5 2D 1H-1H TOCSY 1mM RNA-6, 10mM potassium phosphate-7, 100mM potassium chloride-8, 0.01mM DSS-9, 3mM sodium azide-10, 95% H2O/5% D2O 100% D2O 0.1 6.2 ambient atm 303 6 2D DQF-COSY 1mM RNA-6, 10mM potassium phosphate-7, 100mM potassium chloride-8, 0.01mM DSS-9, 3mM sodium azide-10, 95% H2O/5% D2O 100% D2O 0.1 6.2 ambient atm 303 7 2D 1H-13C HSQC 1mM RNA-6, 10mM potassium phosphate-7, 100mM potassium chloride-8, 0.01mM DSS-9, 3mM sodium azide-10, 95% H2O/5% D2O 100% D2O 0.1 6.2 ambient atm 303 8 JRHMBC 1mM RNA-1, 10mM potassium phosphate-2, 100mM potassium chloride-3, 0.01mM DSS-4, 3mM sodium azide-5 95% H2O/5% D2O 0.1 6.2 ambient atm 303
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker DRX 800 2 Bruker DRX 600
NMR Refinement Method Details Software simulated annealing X-PLOR NIH
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 200 Conformers Submitted Total Number 9 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 structure solution X-PLOR NIH 2.20 Schwieters, Kuszewski, Tjandra and Clore 2 collection XwinNMR Bruker Biospin 3 collection TopSpin Bruker Biospin 4 chemical shift assignment Sparky Goddard 5 peak picking Sparky Goddard 6 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 7 chemical shift assignment PIPP Garrett 8 peak picking PIPP Garrett 9 refinement X-PLOR NIH 2.20 Schwieters, Kuszewski, Tjandra and Clore