6NYY
human m-AAA protease AFG3L2, substrate-bound
ELECTRON MICROSCOPY
| Sample |
|---|
| AFG3L2 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK III |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Sample was blotted for 3 seconds using Whatman No. 1 filter paper immediately prio to plunge-freezing. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 1129437 |
| Reported Resolution (Å) | 3 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Multi-body refinement was used to generate 3 different reconstructions that were stitched together |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6AZ0) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | 85 | ||||
| Fitting Procedure | |||||
| Details | The sequence was threaded onto the PDB ID 6AZ0 and built into the EM density with Coot. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 40 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TECNAI ARCTICA |
| Minimum Defocus (nm) | 8000 |
| Maximum Defocus (nm) | 18000 |
| 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 | 36000 |
| Calibrated Magnification | 43478 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | FindEM | |
| IMAGE ACQUISITION | Leginon | 3.2 |
| CTF CORRECTION | CTFFIND | 4 |
| CTF CORRECTION | RELION | 3.0 |
| MODEL FITTING | UCSF Chimera | 1.11.2 |
| INITIAL EULER ASSIGNMENT | RELION | 3.0 |
| FINAL EULER ASSIGNMENT | RELION | 3.0 |
| RECONSTRUCTION | RELION | 3.0 |
| MODEL REFINEMENT | PHENIX | 1.11.1_2580 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF estimated with CTFFIND 4, local CTF estimated with | 4541491 | Picked with FindEM | |
