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Solution Structure of cis-5R,6S-thymine glycol opposite complementary adenine in duplex DNA
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 20 mM sodium phosphate-1, 100 mM sodium chloride-2, 10 uM sodium azide-3, 50 uM EDTA-4 100% D2O 0.1 7.0 ambient 303 2 2D 1H-1H COSY 20 mM sodium phosphate-1, 100 mM sodium chloride-2, 10 uM sodium azide-3, 50 uM EDTA-4 100% D2O 0.1 7.0 ambient 303 3 2D 1H-1H NOESY 20 mM sodium phosphate-5, 100 mM sodium chloride-6, 10 uM sodium azide-7, 50 uM EDTA-8 90% H2O/10% D2O 0.1 7.0 ambient 278 4 2D 31P-1H COSY 20 mM sodium phosphate-1, 100 mM sodium chloride-2, 10 uM sodium azide-3, 50 uM EDTA-4 100% D2O 0.1 7.0 ambient 303
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 800 2 Bruker AVANCE 600
NMR Refinement Method Details Software simulated annealing, molecular dynamics Amber
NMR Ensemble Information Conformer Selection Criteria back calculated data agree with experimental NOESY spectrum Conformers Calculated Total Number 10 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, ... and Kollm 2 data analysis Sparky Goddard 3 chemical shift assignment Sparky Goddard 4 processing TopSpin Bruker Biospin 5 restraint generation MARDIGRAS Borgias, B.A. & James, T.L. 6 structure validation CORMA James T.L. 7 structure analysis Curves Lavery, R. and Sklenar, H 8 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax