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 | ||||
