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NMR Structure of the Active Conformation of the VS Ribozyme Cleavage Site
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 3D 13C/15N-edited HSQC-NOESY 1.1 mM RNA U-13C,15N; 10 mM d11-Tris pH 7.0; 50 mM NaCl; 0.2 mM EDTA; 0.05 mM NaN3 90% H2O/10% D2O 50mM NaCl 7.0 ambient 298 2 3D 13C-edited HMQC-NOESY 1.1 mM RNA U-13C,15N; 10 mM d11-Tris pH 7.0; 50 mM NaCl; 0.2 mM EDTA; 0.05 mM NaN3 100% D2O 50mM NaCl 7.0 ambient 298 3 2D 1H/15N CPMG-NOESY 1.7 mM RNA U-15N; 10 mM d11-Tris pH 7.0; 50 mM NaCl; 0.2 mM EDTA; 0.05 mM NaN3 90% H2O/10% D2O 50mM NaCl 7.0 ambient 298 4 2D HNN-COSY 1.7 mM RNA U-15N; 10 mM d11-Tris pH 7.0; 50 mM NaCl; 0.2 mM EDTA; 0.05 mM NaN3 90% H2O/10% D2O 50mM NaCl 7.0 ambient 298 5 2D H(CN)N(H) 5.3 mM RNA U-15N; 10 mM d11-Tris pH 7.0; 50 mM NaCl; 0.2 mM EDTA; 0.05mM NaN3 90% H2O/10% D2O 50mM NaCl 7.0 ambient 298 6 2D DQF-COSY 1.7 mM RNA; 10 mM d11-Tris pH 7.0; 50 mM NaCl; 0.2 mM EDTA; 0.05 mM NaN3 100% D2O 50mM NaCl 7.0 ambient 298
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Varian INOVA 600
NMR Refinement Method Details Software restrained molecular dynamics; simulated annealing the first model is the minimized average structure, the last 10
represent the ensemble of structures NMRPipe
NMR Ensemble Information Conformer Selection Criteria structures with the least restraint violations Conformers Calculated Total Number 50 Conformers Submitted Total Number 11 Representative Model 1 (minimized average structure)
Additional NMR Experimental Information Details The structure was determined using triple-resonance NMR spectroscopy
Computation: NMR Software # Classification Version Software Name Author 1 processing NMRPipe 2.1 Delaglio 2 data analysis NMRView 5.03 Johnson 3 structure solution X-PLOR 3.840 Brunger 4 data analysis MOLMOL 2K.1 Koradi 5 refinement X-PLOR 3.840 Brunger