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NMR determination of the 2:1 binding motif structure involving cytosine flipping out for the recognition of the CGG/CGG triad DNA
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D NOESY (200 ms) 2.5 mM NCD-GG1, 20 mM sodium phosphate, 100 mM sodium chloride 90% H2O/10% D2O 120 mM 6.8 1 atm 283 Bruker DRX 800 2 2D 1H-13C HSQC 2.5 mM NCD-GG1, 20 mM sodium phosphate, 100 mM sodium chloride 90% H2O/10% D2O 120 mM 6.8 1 atm 283 Bruker AVANCE 500 3 2D 1H-31P HSQC 2.5 mM NCD-GG1, 20 mM sodium phosphate, 100 mM sodium chloride 90% H2O/10% D2O 120 mM 6.8 1 atm 283 Bruker DRX 800 4 2D DQF-COSY 2.5 mM NCD-GG1, 20 mM sodium phosphate, 100 mM sodium chloride 90% H2O/10% D2O 120 mM 6.8 1 atm 283 Bruker DRX 800 5 2D TOCSY 2.5 mM NCD-GG1, 20 mM sodium phosphate, 100 mM sodium chloride 90% H2O/10% D2O 120 mM 6.8 1 atm 283 Bruker DRX 800 6 2D NOESY (30 ms) 2.5 mM NCD-GG1, 20 mM sodium phosphate, 100 mM sodium chloride 90% H2O/10% D2O 120 mM 6.8 1 atm 283 Bruker DRX 800
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker DRX 800 2 Bruker AVANCE 500
NMR Refinement Method Details Software simulated annealing CNS
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 200 Conformers Submitted Total Number 30 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 collection XwinNMR Bruker Biospin 2 chemical shift assignment NMRFAM-SPARKY Lee W, Tonelli M, Markley JL 3 structure calculation CNS Brunger, Adams, Clore, Gros, Nilges and Read 4 peak picking NMRFAM-SPARKY Lee W, Tonelli M, Markley JL 5 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax