2JSV

Dipole tensor-based refinement for atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR spectroscopy


SOLID-STATE NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
1CC 2D DARR Mixing14 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 H2OH2O5.5ambient281
2CC 2D DARR Mixing14 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 H2OH2O5.5ambient281
3NN 2D PDSD Mixing14 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 H2OH2O5.5ambient281
4HN-HN VEAN14 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 H2OH2O5.5ambient281
5HN-NCA-HA VEAN14 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 H2OH2O5.5ambient281
6NCACX, NCOCX 3D14 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 H2OH2O5.5ambient281
7N(HH)C; C(HH)C14 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 H2OH2O5.5ambient281
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1VarianINOVA750
2VarianInfinity Plus600
3VarianInfinity Plus500
NMR Refinement
MethodDetailsSoftware
DGSA-distance geometry simulated annealing, simulated annealing50,000 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 sizeX-PLOR_NIH
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number260
Conformers Submitted Total Number10
Representative Model1 (lowest energy)
Additional NMR Experimental Information
DetailsThe precipitant was packed with excess mother liquor for data acquisition.
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1structure solutionX-PLOR_NIH2.16.0Schwieters, Kuszewski, Tjandra and Clore
2refinementX-PLOR_NIH2.16.0Schwieters, Kuszewski, Tjandra and Clore
3geometry optimizationX-PLOR_NIH2.16.0Schwieters, Kuszewski, Tjandra and Clore
4processingNMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
5chemical shift assignmentSPARKYGoddard
6data analysisProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss