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NMR STRUCTURE OF THE R(GGAGGACAUCCCUCACGGGUGACCGUGGUCCUCC), DOMAIN IV STEM-LOOP B OF ENTEROVIRAL IRES WITH AUCCCU BULGE
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D NOESY 1mM unlabeled RNA, 25mM NaCl, 25mM sodium phosphate buffer (pH 6.5), 90% H2O, 10% D2O 90% H2O/10% D2O 50 mM Na+ ions 6.5 ambient 283 2 2D NOESY 1mM unlabeled RNA, 25mM NaCl, 25mM sodium phosphate buffer (pH 6.5) D2O 50 mM Na+ ions 6.5 ambient 298 3 DQF-COSY 1mM unlabeled RNA, 25mM NaCl, 25mM sodium phosphate buffer (pH 6.5) D2O 50 mM Na+ ions 6.5 ambient 298 4 3D_13C-separated_NOESY 1mM of uniformly labeled RNA with 13C, 15N, 25mM NaCl, 25mM sodium phosphate buffer (pH 6.5), 90% H2O, 10% D2O 90% H2O/10% D2O 50 mM Na+ ions 6.5 ambient 298 5 1H-13C CONSTANT TIME HSQC 1mM of uniformly labeled RNA with 13C, 15N, 25mM NaCl, 25mM sodium phosphate buffer (pH 6.5), 5% (weight/volume) of C12E6/n-hexanol mixture (molar ratio 0.64) D2O 50 mM Na+ ions 6.5 ambient 298
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Varian INOVA 600
NMR Refinement Method Details Software FULL MATRIX RELAXATION ANALYSIS OF NOE, RANDOM ERROR ANALYSIS OF NOE, SIMULATED ANNEALING USING RESTRAINED MOLECULAR DYNAMICS STRUCTURES ARE REFINED BASED ON 575 NOE-DERIVED DISTANCES AND 86 RESIDUAL DIPOLAR COUPLINGS VNMR
NMR Ensemble Information Conformer Selection Criteria LOWEST TOTAL ENERGY (A WEIGHTED SUM OF CONFORMATIONAL ENERGY AND RESTRAINT ENERGY) Conformers Calculated Total Number 50 Conformers Submitted Total Number 20 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 collection VNMR 6.1 Varian Associates, Inc. 2 processing NMRPipe 2.1 F.Delaglio 3 iterative matrix relaxation MARDIGRAS 3.2 T.L.James 4 refinement DYANA 1.5 P.Guntert 5 refinement Amber 7 D.A.Case