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NMR Localization of Divalent Cations at the Active Site of the Neurospora VS Ribozyme Provides Insights Into RNA-Metal Ion Interactions
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-15N HSQC 1 mM [U-100% 15N] RNA 90% H2O/10% D2O 5 mM Mg2+, 50 mM potassium chloride 6.5 ambient 288 2 2D 1H-15N HSQC NH2 only 1 mM [U-100% 15N] RNA 90% H2O/10% D2O 5 mM Mg2+, 50 mM potassium chloride 6.5 ambient 288 3 2D 1H-13C HSQC 0.9 mM [U-100% 13C; U-100% 15N] RNA 100% D2O 5 mM Mg2+, 50 mM potassium chloride 6.5 ambient 298 4 2D 1H-15N HSQC long-range 0.9 mM [U-100% 13C; U-100% 15N] RNA 90% H2O/10% D2O 5 mM Mg2+, 50 mM potassium chloride 6.5 ambient 288 5 1D 31P 0.2-0.4 mM phosphorothioate RNA 90% H2O/10% D2O 5 mM Mg2+/Cd2+, 50 mM potassium chloride 6.5 ambient 298
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Varian INOVA 500 2 Varian INOVA 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 500 Conformers Submitted Total Number 21 Representative Model 1 (minimized average structure)
Computation: NMR Software # Classification Version Software Name Author 1 structure solution X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 2 data analysis NMRView Johnson, One Moon Scientific 3 data analysis NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 4 refinement X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore