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Solution structure of the DNA Decamer Duplex Containing Double TG Mismatches of Cis-syn Cyclobutane Pyrimidine Dimer
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D NOESY 1mM CPD/GG duplex, nonlabeled, 20mM phosphate buffer, 100mM NaCl 90% H2O, 10% D20 100mM NaCl 7.0 ambient 274 2 2D TOCSY 1mM CPD/GG duplex, nonlabeled, 20mM phosphate buffer, 100mM NaCl 100% D2O 100mM NaCl 7.0 ambient 290 3 DQF-COSY 1mM CPD/GG duplex, nonlabeled, 20mM phosphate buffer, 100mM NaCl 100% D2O 100mM NaCl 7.0 ambient 290 4 2D NOESY 1mM CPD/GG duplex, nonlabeled, 20mM phosphate buffer, 100mM NaCl 90% H2O, 10% D20 100mM NaCl 7.0 ambient 290 5 Natural Abundance 1H-13C HSQC 1mM CPD/GG duplex, nonlabeled, 20mM phosphate buffer, 100mM NaCl 100% D2O 100mM NaCl 7.0 ambient 298
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Varian INOVA 600 2 Bruker DRX 800
NMR Refinement Method Details Software simulated annealing the structures are based on a 500 NOE-derived distance constraints, 112 dihedral angle restraints, 13 residual dipolar coupling restraints NMRPipe
NMR Ensemble Information Conformer Selection Criteria structures with the least restraint violations, structures with the lowest energy Conformers Calculated Total Number 40 Conformers Submitted Total Number 12 Representative Model 4 (fewest violations)
Computation: NMR Software # Classification Version Software Name Author 1 processing NMRPipe 2.1 F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Bax 2 collection VNMR 6.1 Varian, Inc. 3 refinement XPLOR-NIH 2.9.4a G. Marius Clore , John Kuszewski, Charles D. Schwieters, and Nico Tjandra 4 structure solution X-PLOR 3.1 Brunger