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