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Solution structure of oxidized dimeric form of human defensin 5
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-15N HSQC 0.5 mM [U-99% 13C; U-99% 15N] protein 90% H2O/10% D2O 0 4 ambient 298 2 3D HNCA 0.5 mM [U-99% 13C; U-99% 15N] protein 90% H2O/10% D2O 0 4 ambient 298 3 3D HNCO 0.5 mM [U-99% 13C; U-99% 15N] protein 90% H2O/10% D2O 0 4 ambient 298 4 3D HCACO 0.5 mM [U-99% 13C; U-99% 15N] protein 90% H2O/10% D2O 0 4 ambient 298 5 3D HNCACB 0.5 mM [U-99% 13C; U-99% 15N] protein 90% H2O/10% D2O 0 4 ambient 298 6 3D HCCH-TOCSY 0.5 mM [U-99% 13C; U-99% 15N] protein 90% H2O/10% D2O 0 4 ambient 298 7 3D C(CO)NH 0.5 mM [U-99% 13C; U-99% 15N] protein 90% H2O/10% D2O 0 4 ambient 298 8 3D H(CCO)NH 0.5 mM [U-99% 13C; U-99% 15N] protein 90% H2O/10% D2O 0 4 ambient 298 9 3D HNHB 0.5 mM [U-99% 13C; U-99% 15N] protein 90% H2O/10% D2O 0 4 ambient 298 10 3D 1H-15N NOESY 0.5 mM [U-99% 13C; U-99% 15N] protein 90% H2O/10% D2O 0 4 ambient 298 11 3D 1H-13C NOESY 0.5 mM [U-99% 13C; U-99% 15N] protein 90% H2O/10% D2O 0 4 ambient 298 12 2D 1H-15N HSQC 0.3 mM [U-99% 13C; U-99% 15N] protein, 0.3 mM protein 90% H2O/10% D2O 0 4 ambient 298 13 2D 1H-1H NOESY 0.3 mM [U-99% 13C; U-99% 15N] protein, 0.3 mM protein 90% H2O/10% D2O 0 4 ambient 298
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 600 2 Varian AVANCE 500
NMR Refinement Method Details Software simulated annealing, molecular dynamics Initial structures calculated by minimizing target function. Final CYANA structure refined in explicit water using molecular dynamics. NMRPipe
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 100 Conformers Submitted Total Number 20 Representative Model 1 (closest to the average)
Computation: NMR Software # Classification Version Software Name Author 1 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 2 data analysis XEASY Bartels et al. 3 chemical shift assignment XEASY Bartels et al. 4 peak picking XEASY Bartels et al. 5 chemical shift calculation CYANA Guntert, Mumenthaler and Wuthrich 6 structure solution CYANA Guntert, Mumenthaler and Wuthrich 7 structure solution X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 8 refinement X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 9 refinement WHAT IF Vriend 10 refinement CYANA Guntert, Mumenthaler and Wuthrich