Amyloid-beta(1-40) fibril derived from Alzheimer's disease cortical tissue
ELECTRON MICROSCOPY - SOLID-STATE NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 3D NCACX | 100 uM U-15N,13C amyloid-beta(1-40) | phosphate buffer | 10 mM | 7.4 | 1 atm | 297 | Varian InfinityPlus 600 |
| 2 | 3D NCOCX | 100 uM U-15N,13C amyloid-beta(1-40) | phosphate buffer | 10 mM | 7.4 | 1 atm | 297 | Varian InfinityPlus 600 |
| 3 | 3D CANCX | 100 uM U-15N,13C amyloid-beta(1-40) | phosphate buffer | 10 mM | 7.4 | 1 atm | 297 | Varian InfinityPlus 600 |
| 4 | 3D CONCX | 100 uM U-15N,13C amyloid-beta(1-40) | phosphate buffer | 10 mM | 7.4 | 1 atm | 297 | Varian InfinityPlus 600 |
| 5 | 2D 13C-13C | 100 uM U-15N,13C amyloid-beta(1-40) | phosphate buffer | 10 mM | 7.4 | 1 atm | 297 | Varian InfinityPlus 600 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | InfinityPlus | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | phi/psi from TalosN & EM density used as restraints | X-PLOR NIH |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the least restraint violations |
| Conformers Calculated Total Number | 60 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 2 | chemical shift assignment | Sparky | Goddard | |
| 3 | refinement | X-PLOR NIH | 2.53 | Schwieters, Kuszewski, Tjandra and Clore |
| Sample |
|---|
| amyloid-beta(1-40) fibrils derived from human AD brain |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | FILAMENT |
| Vitrification Instrument | LEICA PLUNGER |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | The grids were preblotted for 10 seconds and blotted for 6 seconds before plunging. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 14775 |
| Reported Resolution (Å) | 2.77 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | A modified version of RELION 3.0-beta was used for the reconstruction. The modified version allowed local averaging of the rotation angle. Final rec ... |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | C1 |
| Axial Rise | 2.45 |
| Angular Rotation | 179.66 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | AB INITIO MODEL | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Xplor-NIH was used to combine EM density with phi/psi restraints from NMR chemical shifts (from Talos-N Version 4.21 Rev 2016.343.11.31). | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 QUANTUM (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 73.5 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | -500 |
| Maximum Defocus (nm) | -3000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 130000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | Preliminary grid screening was done manually in FEI T12. |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | 3.0 |
| IMAGE ACQUISITION | SerialEM | v3.7 |
| CTF CORRECTION | Gctf | |
| MODEL FITTING | Coot | 0.8.9 |
| MODEL REFINEMENT | X-PLOR | 2.53 |
| INITIAL EULER ASSIGNMENT | RELION | 3.0 |
| INITIAL EULER ASSIGNMENT | MATLAB | |
| CLASSIFICATION | RELION | custom |
| RECONSTRUCTION | RELION | custom |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | The correction was done in Gctf and is corrected for amplitude. Per -particle CTF refinement was done prior to final reconstruction. | 19790 | The particles were picked using Relion manual pick, with a 20A low pass filter and particle diameter of 30A. | |
