Atomic-resolution structure of a doublet 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/water solution | | 2 | ambient | | |
2 | REDOR | 15 mg/mL [U-100% 13C; U-100% 15N] TTR(105-115) | 10% acetonitrile/water solution | | 2 | ambient | | |
3 | ZF-TEDOR | 15 mg/mL [U-100% 13C; U-100% 15N] TTR(105-115) | 10% acetonitrile/water solution | | 2 | ambient | | |
4 | 2D PDSD | 15 mg/mL [U-100% 13C; U-100% 15N] TTR(105-115) | 10% acetonitrile/water solution | | 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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Doublet 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 | 82 |
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Reported Resolution (Å) | 12.7 |
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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 | | |