☰ Navigation Tabs
Dipole tensor-based refinement for atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR spectroscopy
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 CC 2D DARR Mixing 14 mg/mL (1,3) 13C glycerol, U15N protein, (4R)-2-Metylpentane-2,4-Diol (50% v/v), Isopropyl alcohol (25% v/v), 25 mg/mL GB1 in 50 mM sodium phosphate buffered H2O H2O 5.5 ambient 281 2 CC 2D DARR Mixing 14 mg/mL 2 13C glycerol, Uniform 15N protein, (4R)-2-Metylpentane-2,4-Diol (50% v/v), Isopropyl alcohol (25% v/v), 25 mg/mL GB1 in 50 mM sodium phosphate buffered H2O H2O 5.5 ambient 281 3 NN 2D PDSD Mixing 14 mg/mL [U-99% 15N] protein, (4R)-2-Metylpentane-2,4-Diol (50% v/v), Isopropyl alcohol (25% v/v), 25 mg/mL GB1 in 50 mM sodium phosphate buffered H2O H2O 5.5 ambient 281 4 HN-HN VEAN 14 mg/mL [U-99% 15N] protein, (4R)-2-Metylpentane-2,4-Diol (50% v/v), Isopropyl alcohol (25% v/v), 25 mg/mL GB1 in 50 mM sodium phosphate buffered H2O H2O 5.5 ambient 281 5 HN-NCA-HA VEAN 14 mg/mL [U-99% 13C; U-99% 15N] protein, (4R)-2-Metylpentane-2,4-Diol (50% v/v), Isopropyl alcohol (25% v/v), 25 mg/mL GB1 in 50 mM sodium phosphate buffered H2O H2O 5.5 ambient 281 6 NCACX, NCOCX 3D 14 mg/mL [U-99% 13C; U-99% 15N] protein, (4R)-2-Metylpentane-2,4-Diol (50% v/v), Isopropyl alcohol (25% v/v), 25 mg/mL GB1 in 50 mM sodium phosphate buffered H2O H2O 5.5 ambient 281 7 N(HH)C; C(HH)C 14 mg/mL [U-100% 13C; U-100% 15N] protein, (4R)-2-Metylpentane-2,4-Diol (50% v/v), Isopropyl alcohol (25% v/v), 25 mg/mL GB1 in 50 mM sodium phosphate buffered H2O H2O 5.5 ambient 281
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Varian INOVA 750 2 Varian Infinity Plus 600 3 Varian Infinity Plus 500
NMR Refinement Method Details Software DGSA-distance geometry simulated annealing, simulated annealing 50,000 steps at 2500 K, decreased over 25,000 steps to 1000 K, 1 fs step size, 70,000 steps from 1000K to 300 K, 1 fs step size X-PLOR NIH
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 260 Conformers Submitted Total Number 10 Representative Model 1 (lowest energy)
Additional NMR Experimental Information Details The precipitant was packed with excess mother liquor for data acquisition.
Computation: NMR Software # Classification Version Software Name Author 1 structure solution X-PLOR NIH 2.16.0 Schwieters, Kuszewski, Tjandra and Clore 2 refinement X-PLOR NIH 2.16.0 Schwieters, Kuszewski, Tjandra and Clore 3 geometry optimization X-PLOR NIH 2.16.0 Schwieters, Kuszewski, Tjandra and Clore 4 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 5 chemical shift assignment Sparky Goddard 6 data analysis Procheck Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss