Encapsulin 2 of a two-component Family 2B encapsulin shell from Streptomyces lydicus
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 9BHU | |
| Sample |
|---|
| A two-component Family 2B encapsulin shell from Streptomyces lydicus with enriched encapsulin 2 |
| Sample Components |
| Encapsulin 1 of a two-component Family 2B encapsulin shell from Streptomyces lydicus |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Blot force: 20 Blot time: 4 seconds Wait time: 0 seconds |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 155190 |
| Reported Resolution (Å) | 2.59 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | The map was generated by homogeneous refinement against the initial ab-initio map using I symmetry, per-particle defocus optimization, and per-group C ... |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (9BHU) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | correlation coefficient | ||||
| Overall B Value | 114.4 | ||||
| Fitting Procedure | |||||
| Details | The starting encapsulin model was first placed into the map using ChimeraX. It was then refined against the map by alternating rounds of manual refine ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 54 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 500 |
| Maximum Defocus (nm) | 1000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| 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 | v3.1.0 |
| IMAGE ACQUISITION | Leginon | |
| CTF CORRECTION | cryoSPARC | v3.1.0 |
| MODEL FITTING | UCSF ChimeraX | v 1.2.5 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | v3.1.0 |
| FINAL EULER ASSIGNMENT | cryoSPARC | v3.1.0 |
| RECONSTRUCTION | cryoSPARC | v3.1.0 |
| MODEL REFINEMENT | Coot | 0.8.9.1 |
| MODEL REFINEMENT | PHENIX | 1.20.1-4487 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 288651 | |||
