6R4R
Cryo-EM Structure of the PI3-Kinase SH3 Domain Amyloid Fibril
ELECTRON MICROSCOPY
| Sample |
|---|
| Fibril of PI3K-SH3 domains |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | FILAMENT |
| Vitrification Instrument | |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 27681 |
| Reported Resolution (Å) | 3.4 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | For the even/odd test, the segment images were split by entire fibrils and refined separately for 25 iterations using the same reference density (low- ... |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | C1 |
| Axial Rise | 2.3548 |
| Angular Rotation | 179.436 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | AB INITIO MODEL | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON III (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 26 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TECNAI ARCTICA |
| Minimum Defocus (nm) | |
| Maximum Defocus (nm) | |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | EPU | 1.2.0.16 |
| CTF CORRECTION | CTFFIND | 4.1.10 |
| MODEL FITTING | Coot | |
| FINAL EULER ASSIGNMENT | RELION | 2 |
| CLASSIFICATION | RELION | 2 |
| RECONSTRUCTION | RELION | 2 |
| MODEL REFINEMENT | PHENIX | 1.13_2998 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 103733 | Filaments were picked manually in Relion2 | ||
