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The Structure of RNA Internal Loops with Tandem AG Pairs: 5'AAGU/3'UGAA
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 1 mM RNA (5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3')-1, 80 mM sodium chloride-2, 10 mM sodium phosphate-3, 0.5 mM EDTA-4 90% H2O/10% D2O 0.1 6.1 ambient 273 2 2D 1H-13C HSQC 1 mM RNA (5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3')-1, 80 mM sodium chloride-2, 10 mM sodium phosphate-3, 0.5 mM EDTA-4 90% H2O/10% D2O 0.1 6.1 ambient 273 3 2D 1H-1H TOCSY 1 mM RNA (5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3')-5, 80 mM sodium chloride-6, 10 mM sodium phosphate-7, 0.5 mM EDTA-8 100% D2O 0.1 6.1 ambient 283 4 2D DQF-COSY 1 mM RNA (5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3')-5, 80 mM sodium chloride-6, 10 mM sodium phosphate-7, 0.5 mM EDTA-8 100% D2O 0.1 6.1 ambient 283 5 2D 1H-31P HETCOR 1 mM RNA (5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3')-5, 80 mM sodium chloride-6, 10 mM sodium phosphate-7, 0.5 mM EDTA-8 100% D2O 0.1 6.1 ambient 283 6 2D 1H-1H NOESY 1 mM RNA (5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3')-5, 80 mM sodium chloride-6, 10 mM sodium phosphate-7, 0.5 mM EDTA-8 100% D2O 0.1 6.1 ambient 283
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Varian INOVA 600 2 Varian INOVA 500
NMR Refinement Method Details Software simulated annealing Sparky
NMR Ensemble Information Conformer Selection Criteria structures with the least restraint violations Conformers Calculated Total Number 40 Conformers Submitted Total Number 7 Representative Model 1 (closest to the average)
Computation: NMR Software # Classification Version Software Name Author 1 chemical shift assignment Sparky 3.12 Goddard 2 data analysis Sparky 3.12 Goddard 3 collection VNMR 6.1C Varian 4 structure solution CNS 1.2 Brunger, Adams, Clore, Gros, Nilges and Read 5 refinement Amber 9 Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm