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NMR structure for Sp1 transcription factor duplex 5'-d(GGGGCGGGG)
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D DQF-COSY 1.0 mM DNA, 25 mM sodium chloride, 5 mM Na Phoshate, 0.5 mM EDTA 100% D2O 30 mM Na+ mM 7.0 1 atm 298 Bruker AVANCE 800 2 2D 1H-1H TOCSY 1.0 mM DNA, 25 mM sodium chloride, 5 mM Na Phoshate, 0.5 mM EDTA 100% D2O 30 mM Na+ mM 7.0 1 atm 298 Bruker AVANCE 800 3 2D 1H-13C HSQC 1.0 mM DNA, 25 mM sodium chloride, 5 mM Na Phoshate, 0.5 mM EDTA 100% D2O 30 mM Na+ mM 7.0 1 atm 298 Bruker AVANCE 800 4 2D 1H-1H NOESY 1.0 mM DNA, 25 mM sodium chloride, 5 mM Na Phoshate, 0.5 mM EDTA 100% D2O 30 mM Na+ mM 7.0 1 atm 298 Bruker AVANCE 800 5 2D 1H-1H NOESY 680 uM DNA, 25 mM sodium chloride, 5 mM Na Phosphate, 0.5 mM EDTA 90% H2O/10% D2O 30 mM Na+ mM 7.0 1 atm 298 Bruker AVANCE III 850 6 2D ECOSY 1.0 mM DNA, 25 mM sodium chloride, 5 mM Na Phoshate, 0.5 mM EDTA 100% D2O 30 mM Na+ mM 7.0 1 atm 298 Bruker AVANCE III 850 7 2D PhCOSY 1.0 mM DNA, 25 mM sodium chloride, 5 mM Na Phoshate, 0.5 mM EDTA 100% D2O 30 mM Na+ mM 7.0 1 atm 298 Bruker AVANCE II 600 8 2D PhTOCSY 1.0 mM DNA, 25 mM sodium chloride, 5 mM Na Phoshate, 0.5 mM EDTA 100% D2O 30 mM Na+ mM 7.0 1 atm 298 Bruker AVANCE II 600
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 800 3 Bruker AVANCE III 850 2 Bruker AVANCE II 600
NMR Refinement Method Details Software simulated annealing 214 NOE distance constraints, 54 hydrogen distance restraints, 48 dihedral angle restraints. Amber
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 20 Conformers Submitted Total Number 20 Representative Model 1 (closest to the average)
Computation: NMR Software # Classification Version Software Name Author 1 refinement Amber 14.0 Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman 2 structure calculation CYANA 3.97 Guntert, Mumenthaler and Wuthrich 3 chemical shift assignment Sparky Goddard 4 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 5 data analysis 3DNA Lu 6 collection TopSpin Bruker Biospin