8FF2
Amyloid-beta (1-40) fibrils derived from a CAA patient
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6SHS | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 10.634 |
| f_angle_d | 0.41 |
| f_chiral_restr | 0.044 |
| f_bond_d | 0.005 |
| f_plane_restr | 0.002 |
| Sample |
|---|
| Fibrillar assembly of human Amyloid-beta 1-40 derived from vascular deposits in a cerebral amyloid angiopathy patient |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | FILAMENT |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 59075 |
| Reported Resolution (Å) | 2.87 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | C1 |
| Axial Rise | 2.44 |
| Angular Rotation | -178.83 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6SHS) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | AB INITIO MODEL | ||||
| Refinement Target | |||||
| Overall B Value | 31.1 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON III (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 49.7 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TALOS ARCTICA |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 1400 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 92000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | 3.1.1 |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | Gctf | 1.06 |
| CTF CORRECTION | RELION | 3.1.1 |
| MODEL FITTING | Coot | |
| MODEL REFINEMENT | PHENIX | 1.19.1 |
| MODEL REFINEMENT | ISOLDE | 1.4 |
| INITIAL EULER ASSIGNMENT | RELION | 3.1.1 |
| FINAL EULER ASSIGNMENT | RELION | 3.1.1 |
| CLASSIFICATION | RELION | 3.1.1 |
| RECONSTRUCTION | RELION | 3.1.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | Per-micrograph correction via Gctf. Aberration, magnification, and per-particle corrections via RELION. | 68357 | Manual helical picking and extraction | |
