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NMR solution structure of HIV-1 nucleocapsid protein in complex with an inhibitor displaying a 2 inhibitors:1 NC stoichiometry
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 3D HNCA 250 uM [U-100% 13C; U-100% 15N] protein, 500 uM inhibitor 90% H2O/10% D2O 0.025 6.5 ambient 300 2 3D HNCACB 250 uM [U-100% 13C; U-100% 15N] protein, 500 uM inhibitor 90% H2O/10% D2O 0.025 6.5 ambient 300 3 2D DQF-COSY 250 uM [U-100% 13C; U-100% 15N] protein, 500 uM inhibitor 90% H2O/10% D2O 0.025 6.5 ambient 300 4 2D 1H-1H NOESY 250 uM [U-100% 13C; U-100% 15N] protein, 500 uM inhibitor 90% H2O/10% D2O 0.025 6.5 ambient 300 5 2D 1H-15N HSQC 250 uM [U-100% 13C; U-100% 15N] protein, 500 uM inhibitor 90% H2O/10% D2O 0.025 6.5 ambient 300 6 3D CBCA(CO)NH 250 uM [U-100% 13C; U-100% 15N] protein, 500 uM inhibitor 90% H2O/10% D2O 0.025 6.5 ambient 300 7 3D HCCH-TOCSY 250 uM [U-100% 13C; U-100% 15N] protein, 500 uM inhibitor 90% H2O/10% D2O 0.025 6.5 ambient 300 8 3D 1H-15N NOESY 250 uM [U-100% 13C; U-100% 15N] protein, 500 uM inhibitor 90% H2O/10% D2O 0.025 6.5 ambient 300 9 3D 1H-13C NOESY aliphatic 250 uM [U-100% 13C; U-100% 15N] protein, 500 uM inhibitor 90% H2O/10% D2O 0.025 6.5 ambient 300
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 600
NMR Refinement Method Details Software simulated annealing Amber
NMR Ensemble Information Conformer Selection Criteria structures with the least restraint violations Conformers Calculated Total Number 100 Conformers Submitted Total Number 10 Representative Model 1 (fewest violations)
Computation: NMR Software # Classification Version Software Name Author 1 structure solution Amber 8.0 Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman 2 refinement Amber Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman