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NMR model of the first let-7 miRNA complementary site (LCS1) in 3'-UTR of lin-41 mRNA from C. elegans
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D NOESY 2mM [U-100% 13C; U-100% 15N] RNA (34-MER)-4, 10mM sodium phosphate-5, 20mM sodium chloride-6 100% D2O 20 6.8 ambient 303 2 2D 15N-HSQC 2mM [U-100% 13C; U-100% 15N] RNA (34-MER)-1, 10mM sodium phosphate-2, 20mM sodium chloride-3 95% H2O/5% D2O 20 6.8 ambient 278 3 2D 13C-HSQC 2mM [U-100% 13C; U-100% 15N] RNA (34-MER)-4, 10mM sodium phosphate-5, 20mM sodium chloride-6 100% D2O 20 6.8 ambient 303 4 2D DQF-COSY 2mM [U-100% 13C; U-100% 15N] RNA (34-MER)-4, 10mM sodium phosphate-5, 20mM sodium chloride-6 100% D2O 20 6.8 ambient 303 5 2D HNN-COSY 2mM [U-100% 13C; U-100% 15N] RNA (34-MER)-1, 10mM sodium phosphate-2, 20mM sodium chloride-3 95% H2O/5% D2O 20 6.8 ambient 278 6 2D TOCSY 2mM [U-100% 13C; U-100% 15N] RNA (34-MER)-4, 10mM sodium phosphate-5, 20mM sodium chloride-6 100% D2O 20 6.8 ambient 303 7 2D 1H-31P COSY 2mM [U-100% 13C; U-100% 15N] RNA (34-MER)-4, 10mM sodium phosphate-5, 20mM sodium chloride-6 100% D2O 20 6.8 ambient 303 8 2D 15N-IPAP-HSQC 1mM [U-100% 13C; U-100% 15N] RNA (34-MER)-7, 10mM sodium phosphate-8, 20mM sodium chloride-9, 17mg/mL Pf1 phage-10 90% H2O/10% D2O 20 6.8 ambient 303 9 3D HCCH-TOCSY 2mM [U-100% 13C; U-100% 15N] RNA (34-MER)-4, 10mM sodium phosphate-5, 20mM sodium chloride-6 100% D2O 20 6.8 ambient 303 10 3D HCCH-COSY 2mM [U-100% 13C; U-100% 15N] RNA (34-MER)-4, 10mM sodium phosphate-5, 20mM sodium chloride-6 100% D2O 20 6.8 ambient 303 11 3D 13C-separated-NOESY 2mM [U-100% 13C; U-100% 15N] RNA (34-MER)-4, 10mM sodium phosphate-5, 20mM sodium chloride-6 100% D2O 20 6.8 ambient 303
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Varian NMR system 800 2 Varian NMR system 600
NMR Refinement Method Details Software simulated annealing, energy minimization 810 NOE-derived distance restraints, 138 torsion angle restraints, 52 residual dipolar coupling restraints, 32 hydrogen bond restraints and 24 planarity restraints. Amber
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy and least restraint violations Conformers Calculated Total Number 100 Conformers Submitted Total Number 10 Representative Model 1 (closest to the average)
Computation: NMR Software # Classification Version Software Name Author 1 refinement Amber 9 Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollm 2 data analysis Felix 2002 Accelrys Software Inc. 3 processing Felix 2002 Accelrys Software Inc. 4 data collection VnmrJ 2.1B Varian