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Solution structure of a double base-pair inversion mutant of murine tumour necrosis factor alpha CDE-23 RNA
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-15N HSQC 0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate 100% D2O 20 6.5 ambient 300 2 2D 1H-13C HSQC 0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate 100% D2O 20 6.5 ambient 300 3 immino-1H-1H NOESY 0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate 90% H2O/10% D2O 20 6.5 ambient 300 4 3D-HCCH-COSY-TOCSY 0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate 100% D2O 20 6.5 ambient 300 5 3D HsCNb/HbCNb 0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate 100% D2O 20 6.5 ambient 300 6 2D HNN-COSY 0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate 90% H2O/10% D2O 20 6.5 ambient 300 7 3D 13C-edited NOESY 0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate 100% D2O 20 6.5 ambient 300 8 2D COSY 0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate 100% D2O 20 6.5 ambient 300 9 1H-31P HET-COR(P,H-COSY-H,C-HMQC) 0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate 100% D2O 20 6.5 ambient 300 10 T1-13C-EDIT relaxation 0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate 100% D2O 20 6.5 ambient 300 11 T1rho-13C-EDIT relaxation 0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate 100% D2O 20 6.5 ambient 300 12 13C-base edited IPAP 0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate, 30 mg/mL Pf1 phage 100% D2O 20 6.5 ambient 300 13 13C-sugar edited IPAP 0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate, 30 mg/mL Pf1 phage 100% D2O 20 6.5 ambient 300
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 700 2 Bruker AVANCE 600 3 Bruker AVANCE 800
NMR Refinement Method Details Software DGSA-distance geometry simulated annealing ARIA
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 100 Conformers Submitted Total Number 10 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 structure solution ARIA 1.2 Linge, O'Donoghue and Nilges 2 chemical shift assignment CCPN_Analysis 2.3 CCPN 3 collection TopSpin 3.0 Bruker Biospin 4 structure solution CNS 1.1 Brunger, Adams, Clore, Gros, Nilges and Read 5 refinement CNS 1.1 Brunger, Adams, Clore, Gros, Nilges and Read