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Structure of the HIV-1 frameshift site RNA bound to a small molecule inhibitor of viral replication
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 0.75 mM RNA (45-MER), 0.75 mM DB213, 20 uM DSS, 20 mM potassium chloride, 10 mM [U-2H] TRIS 90% H2O/10% D2O 20 7.0 ambient atm 283 2 2D 1H-1H NOESY 0.75 mM RNA (45-MER), 0.75 mM DB213, 20 uM DSS, 20 mM potassium chloride, 10 mM [U-2H] TRIS 100% D2O 20 7.0 ambient atm 308 3 2D 1H-1H TOCSY 0.75 mM RNA (45-MER), 0.75 mM DB213, 20 uM DSS, 20 mM potassium chloride, 10 mM [U-2H] TRIS 100% D2O 20 7.0 ambient atm 308 4 2D 1H-13C HSQC 1.5 mM RNA (45-MER), 1.5 mM DB213, 40 uM DSS, 40 mM potassium chloride, 20 mM [U-2H] TRIS 100% D2O 20 7.0 ambient atm 308 5 2D 1H-13C HSQC 1.5 mM RNA (45-MER), 1.5 mM DB213, 40 uM DSS, 40 mM potassium chloride, 20 mM [U-2H] TRIS, 4.5 mg Pf1 phage 100% D2O 20 7.0 ambient atm 308
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker DMX 750 2 Varian AVANCE 900
NMR Refinement Method Details Software torsion angle dynamics, molecular dynamics HADDOCK
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 50 Conformers Submitted Total Number 10 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 docking HADDOCK 2.0 Alexandre Bonvin, Utrecht University 2 refinement HADDOCK 2.0 Alexandre Bonvin, Utrecht University 3 structure solution HADDOCK 2.0 Alexandre Bonvin, Utrecht University 4 refinement Amber 9.0 Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm 5 structure solution Amber 9.0 Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm 6 chemical shift assignment Sparky Goddard 7 data analysis Sparky Goddard 8 peak picking Sparky Goddard 9 data analysis SYBYL 8.0 Tripos 10 geometry optimization SYBYL 8.0 Tripos 11 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 12 collection XwinNMR 3.5 Bruker Biospin 13 processing XwinNMR 3.5 Bruker Biospin 14 collection VnmrJ Varian 15 data analysis PALES Markus Zweckstetter, Ad Bax 16 data analysis PyMOL DeLano Scientific