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RDC and RCSA refinement of an A-form RNA: Improvements in Major Groove Width
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 0.25-1 mM RNA, 0.25 mM [U-100% 13C], [C-100% 13C] RNA, 0.25 mM [G-100% 13C], [A-100% 13C] RNA, 150 mM sodium chloride, 10 mM TRIS 100% D2O 0.15 6.5 ambient 303 2 2D 1H-1H TOCSY 0.25-1 mM RNA, 0.25 mM [U-100% 13C], [C-100% 13C] RNA, 0.25 mM [G-100% 13C], [A-100% 13C] RNA, 150 mM sodium chloride, 10 mM TRIS 100% D2O 0.15 6.5 ambient 303 3 2D 1H-13C HMQC 0.25-1 mM RNA, 0.25 mM [U-100% 13C], [C-100% 13C] RNA, 0.25 mM [G-100% 13C], [A-100% 13C] RNA, 150 mM sodium chloride, 10 mM TRIS 100% D2O 0.15 6.5 ambient 303 4 2D Tr 1H-13C HSQC 0.25-1 mM RNA, 0.25 mM [U-100% 13C], [C-100% 13C] RNA, 0.25 mM [G-100% 13C], [A-100% 13C] RNA, 150 mM sodium chloride, 10 mM TRIS 100% D2O 0.15 6.5 ambient 303 5 2D Tr 1H-13C HSQC 0.25-1 mM RNA, 0.25 mM [U-100% 13C], [C-100% 13C] RNA, 0.25 mM [G-100% 13C], [A-100% 13C] RNA, 150 mM sodium chloride, 10 mM TRIS 100% D2O 0.15 6.5 ambient 303
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 800 2 Bruker DMX 600
NMR Refinement Method Details Software molecular dynamics Amber
NMR Ensemble Information Conformer Selection Criteria structures with the least restraint violations Conformers Calculated Total Number 200 Conformers Submitted Total Number 20 Representative Model 1 (fewest violations)
Computation: NMR Software # Classification Version Software Name Author 1 refinement Amber Case, D. et al. 2 geometry optimization CYANA Guntert, P. et al.