Atomic-resolution structure of a triplet cross-beta amyloid fibril
SOLID-STATE NMR - ELECTRON MICROSCOPY
| NMR Experiment |
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| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
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| 1 | 1D DQ-DRAWS | 15 mg/mL [U-100% 13C; U-100% 15N] TTR(105-115) | 10% acetonitrile/H2O | | 2 | ambient | | |
| 2 | REDOR | 15 mg/mL [U-100% 13C; U-100% 15N] TTR(105-115) | 10% acetonitrile/H2O | | 2 | ambient | | |
| 3 | ZF-TEDOR | 15 mg/mL [U-100% 13C; U-100% 15N] TTR(105-115) | 10% acetonitrile/H2O | | 2 | ambient | | |
| 4 | 2D PDSD | 15 mg/mL [U-100% 13C; U-100% 15N] TTR(105-115) | 10% acetonitrile/H2O | | 2 | ambient | | |
| NMR Spectrometer Information |
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| Spectrometer | Manufacturer | Model | Field Strength |
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| 1 | Bruker | | 900 |
| 2 | | | 750 |
| 3 | | | 500 |
| NMR Refinement |
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| Method | Details | Software |
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| simulated annealing | | CNSSOLVE |
| NMR Ensemble Information |
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| Conformer Selection Criteria | structures with the least restraint violations |
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| Conformers Calculated Total Number | 100 |
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| Conformers Submitted Total Number | 1 |
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| Representative Model | 1 (lowest energy) |
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| Computation: NMR Software |
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| # | Classification | Version | Software Name | Author |
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| 1 | structure solution | CNSSOLVE | | Brunger, Adams, Clore, Gros, Nilges and Read |
| 2 | refinement | CNSSOLVE | | Brunger, Adams, Clore, Gros, Nilges and Read |
| Sample |
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| Triplet cross-beta amyloid fibril polymorph |
| Specimen Preparation |
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| Sample Aggregation State | FILAMENT |
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| Vitrification Instrument | HOMEMADE PLUNGER |
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| Cryogen Name | ETHANE |
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| Sample Vitrification Details | Fibrils were applied to holey carbon films that were immediately plunge-frozen at liquid nitrogen temperature. |
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| 3D Reconstruction |
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| Reconstruction Method | SINGLE PARTICLE |
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| Number of Particles | 152 |
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| Reported Resolution (Å) | 12.2 |
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| Resolution Method | FSC 0.5 CUT-OFF |
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| Other Details | The particles were selected using an automatic selection program. |
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| Refinement Type | |
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| Symmetry Type | HELICAL |
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| Map-Model Fitting and Refinement |
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| Id | 1 |
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| Refinement Space | |
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| Refinement Protocol | |
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| Refinement Target | |
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| Overall B Value | |
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| Fitting Procedure | |
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| Details | |
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| Data Acquisition |
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| Detector Type | KODAK SO-163 FILM |
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| Electron Dose (electrons/Å**2) | |
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| Imaging Experiment | 1 |
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| Date of Experiment | 2006-03-03 |
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| Temperature (Kelvin) | 99 |
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| Microscope Model | FEI TECNAI F20 |
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| Minimum Defocus (nm) | 900 |
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| Maximum Defocus (nm) | 3000 |
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| Minimum Tilt Angle (degrees) | |
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| Maximum Tilt Angle (degrees) | |
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| Nominal CS | |
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| Imaging Mode | BRIGHT FIELD |
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| Specimen Holder Model | GATAN LIQUID NITROGEN |
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| Nominal Magnification | 40000 |
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| Calibrated Magnification | 40000 |
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| Source | FIELD EMISSION GUN |
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| Acceleration Voltage (kV) | 200 |
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| Imaging Details | |
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| EM Software |
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| Task | Software Package | Version |
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| RECONSTRUCTION | BKRP | |
| RECONSTRUCTION | IMAGIC | |
| RECONSTRUCTION | SPIDER | |
| Image Processing |
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| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details |
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| CTFFIND3 | | |
