Atomic-resolution structure of a doublet cross-beta amyloid fibril
SOLID-STATE NMR - ELECTRON MICROSCOPY
| NMR Experiment |
|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
|---|
| 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 |
|---|
| Spectrometer | Manufacturer | Model | Field Strength |
|---|
| 1 | Bruker | | 900 |
| 2 | | | 750 |
| 3 | | | 500 |
| NMR Refinement |
|---|
| Method | Details | Software |
|---|
| simulated annealing | | CNSSOLVE |
| NMR Ensemble Information |
|---|
| Conformer Selection Criteria | structures with the least restraint violations |
|---|
| Conformers Calculated Total Number | 100 |
|---|
| Conformers Submitted Total Number | 1 |
|---|
| Representative Model | 1 (lowest energy) |
|---|
| Computation: NMR Software |
|---|
| # | Classification | Version | Software Name | Author |
|---|
| 1 | structure solution | CNSSOLVE | | Brunger, Adams, Clore, Gros, Nilges and Read |
| 2 | refinement | CNSSOLVE | | Brunger, Adams, Clore, Gros, Nilges and Read |
| Sample |
|---|
| Doublet cross-beta amyloid fibril polymorph |
| Specimen Preparation |
|---|
| Sample Aggregation State | FILAMENT |
|---|
| Vitrification Instrument | HOMEMADE PLUNGER |
|---|
| Cryogen Name | ETHANE |
|---|
| Sample Vitrification Details | Fibrils were applied to holey carbon films that were immediately plunge-frozen at liquid nitrogen temperature. |
|---|
| 3D Reconstruction |
|---|
| Reconstruction Method | SINGLE PARTICLE |
|---|
| Number of Particles | 82 |
|---|
| Reported Resolution (Å) | 12.7 |
|---|
| Resolution Method | FSC 0.5 CUT-OFF |
|---|
| Other Details | The particles were selected using an automatic selection program. |
|---|
| Refinement Type | |
|---|
| Symmetry Type | HELICAL |
|---|
| Map-Model Fitting and Refinement |
|---|
| Id | 1 |
|---|
| Refinement Space | |
|---|
| Refinement Protocol | |
|---|
| Refinement Target | |
|---|
| Overall B Value | |
|---|
| Fitting Procedure | |
|---|
| Details | |
|---|
| Data Acquisition |
|---|
| Detector Type | KODAK SO-163 FILM |
|---|
| Electron Dose (electrons/Å**2) | |
|---|
| Imaging Experiment | 1 |
|---|
| Date of Experiment | 2006-03-03 |
|---|
| Temperature (Kelvin) | 99 |
|---|
| Microscope Model | FEI TECNAI F20 |
|---|
| Minimum Defocus (nm) | 900 |
|---|
| Maximum Defocus (nm) | 3000 |
|---|
| Minimum Tilt Angle (degrees) | |
|---|
| Maximum Tilt Angle (degrees) | |
|---|
| Nominal CS | |
|---|
| Imaging Mode | BRIGHT FIELD |
|---|
| Specimen Holder Model | GATAN LIQUID NITROGEN |
|---|
| Nominal Magnification | 40000 |
|---|
| Calibrated Magnification | 40000 |
|---|
| Source | FIELD EMISSION GUN |
|---|
| Acceleration Voltage (kV) | 200 |
|---|
| Imaging Details | |
|---|
| EM Software |
|---|
| Task | Software Package | Version |
|---|
| RECONSTRUCTION | BKRP | |
| RECONSTRUCTION | IMAGIC | |
| RECONSTRUCTION | SPIDER | |
| Image Processing |
|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details |
|---|
| CTFFIND3 | | |
