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NMR solution structure of midkine-a
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-15N HSQC 10 mM sodium phosphate, 0.1 mM sodium azide, 100 mM sodium chloride, 1 mM EDTA, 0.8 mM [U-100% 13C; U-100% 15N] protein, 95% H2O, 5% D2O 95% H2O/5% D2O 6.5 ambient 303 2 2D 1H-13C HSQC 10 mM sodium phosphate, 0.1 mM sodium azide, 100 mM sodium chloride, 1 mM EDTA, 0.8 mM [U-100% 13C; U-100% 15N] protein, 95% H2O, 5% D2O 95% H2O/5% D2O 6.5 ambient 303 3 3D HN(CO)CA 10 mM sodium phosphate, 0.1 mM sodium azide, 100 mM sodium chloride, 1 mM EDTA, 0.8 mM [U-100% 13C; U-100% 15N] protein, 95% H2O, 5% D2O 95% H2O/5% D2O 6.5 ambient 303 4 3D HNCA 10 mM sodium phosphate, 0.1 mM sodium azide, 100 mM sodium chloride, 1 mM EDTA, 0.8 mM [U-100% 13C; U-100% 15N] protein, 95% H2O, 5% D2O 95% H2O/5% D2O 6.5 ambient 303 5 3D MQ-(H)CCH-TOCSY 10 mM sodium phosphate, 0.1 mM sodium azide, 100 mM sodium chloride, 1 mM EDTA, 0.8 mM [U-100% 13C; U-100% 15N] protein, 95% H2O, 5% D2O 95% H2O/5% D2O 6.5 ambient 303 6 13C/ 15N edited-NOESY 10 mM sodium phosphate, 0.1 mM sodium azide, 100 mM sodium chloride, 1 mM EDTA, 0.8 mM [U-100% 13C; U-100% 15N] protein, 95% H2O, 5% D2O 95% H2O/5% D2O 6.5 ambient 303
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 800
NMR Refinement Method Details Software simulated annealing NOE distance refinement using CYANA 2.1. Hydrogen bond restraints using H-D exchange experiment CYANA
NMR Ensemble Information Conformer Selection Criteria target function Conformers Calculated Total Number 100 Conformers Submitted Total Number 10 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 refinement CYANA 2.1 Guntert P. 2 processing NMRPipe 1 Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 3 data analysis NMRView 5.04 Johnson, One Moon Scientific 4 geometry optimization TALOS Cornilescu, Delaglio and Bax