ELECTRON MICROSCOPY
| Sample |
|---|
| Escherichia coli KTE40 DyP peroxidase-loaded encapsulin shell |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Grids were frozen with a blot force of 20, blot time of 4 seconds, 100% humidity, and chamber temperature of 22 degrees C. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 286236 |
| Reported Resolution (Å) | 2.17 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Homogeneous refinement was used against an ab-initio map with I symmetry, per-particle defocus optimization enabled, per-group CTF parameter optimizat ... |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | cross-correlation coefficient | ||||
| Overall B Value | 85.5 | ||||
| Fitting Procedure | |||||
| Details | The AlphaFold model was placed using ChimeraX, followed by iterative manual refinement in Coot followed by Phenix real space refinements. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 39.91 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 2500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 105000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | v.4.1.2 |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | cryoSPARC | V.4.1.2 |
| MODEL FITTING | UCSF ChimeraX | 1.8 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | v.4.1.2 |
| FINAL EULER ASSIGNMENT | cryoSPARC | v.4.1.2 |
| RECONSTRUCTION | cryoSPARC | v.4.1.2 |
| MODEL REFINEMENT | Coot | 0.9.8 |
| MODEL REFINEMENT | PHENIX | 1.2.1-4487 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 292965 | |||
