☰ Navigation Tabs
Solution Structure of Domain II of the Positive Polarity CCHMVD Hammerhead Ribozyme
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 0.7 mM RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA 90% H2O/10% D2O 12.4 6 ambient 281 2 2D 1H-1H NOESY 0.7 mM RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA 100% D2O 12.4 6 ambient 296 3 2D 1H-1H TOCSY 0.7 mM RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA 100% D2O 12.4 6 ambient 296 4 2D 1H-1H COSY 0.7 mM RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA 100% D2O 12.4 6 ambient 296 5 2D 1H-15N HSQC 0.4 mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA 90% H2O/10% D2O 12.4 6 ambient 281 6 2D 1H-13C HSQC 0.4 mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA 100% D2O 12.4 6 ambient 296 7 3D 1H,13C HMQC-NOESY 0.4 mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA 100% D2O 12.4 6 ambient 296 8 3D HCCH-COSY 0.4 mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA 100% D2O 12.4 6 ambient 296 9 2D HCCH-TOCSY 0.4 mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA 100% D2O 12.4 6 ambient 296 10 3D HCP 0.4 mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA 100% D2O 12.4 6 ambient 296 11 3D 13C-ED-1H-31P HETCOR 0.4 mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA 100% D2O 12.4 6 ambient 296
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 600 2 Bruker AVANCE 600
NMR Refinement Method Details Software simulated annealing and restrained energy minimization minimized average structure of 33 converged conformers with the least restraint violation energy and total energy TopSpin
NMR Ensemble Information Conformer Selection Criteria minimized average structure of 33 converged conformers with the least restraint violation energy and total energy Conformers Calculated Total Number 60 Conformers Submitted Total Number 1 Representative Model 1 (minimized average structure)
Computation: NMR Software # Classification Version Software Name Author 1 collection TopSpin 1.3 Bruker Biospin 2 processing TopSpin 1.3 Bruker Biospin 3 chemical shift assignment Sparky 3.110 Goddard 4 data analysis Sparky 3.110 Goddard 5 structure solution Amber 8.0 Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm 6 refinement Amber 8.0 Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm