8QN6
Amyloid-beta 40 type 2 filament from the leptomeninges of individual with Alzheimer's disease and cerebral amyloid angiopathy
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 7Q4B | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_long_range_B_other | 15.005 |
| r_long_range_B_refined | 14.991 |
| r_scangle_other | 10.483 |
| r_dihedral_angle_3_deg | 8.991 |
| r_mcangle_other | 7.071 |
| r_mcangle_it | 7.054 |
| r_scbond_it | 6.259 |
| r_scbond_other | 6.249 |
| r_dihedral_angle_1_deg | 5.263 |
| r_mcbond_it | 4.574 |
| Sample |
|---|
| Amyloid-beta 40 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | FILAMENT |
| Vitrification Instrument | |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 81140 |
| Reported Resolution (Å) | 2.4 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | C2 |
| Axial Rise | 4.87 |
| Angular Rotation | -0.78 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (7Q4B) | ||||
| Refinement Space | |||||
| Refinement Protocol | |||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON IV (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 40 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 2400 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | 4.0 |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | RELION | |
| MODEL FITTING | Coot | |
| INITIAL EULER ASSIGNMENT | RELION | |
| FINAL EULER ASSIGNMENT | RELION | |
| CLASSIFICATION | RELION | |
| RECONSTRUCTION | RELION | |
| MODEL REFINEMENT | REFMAC | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||
