Encapsulin 1 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 | 9BIX | |
| Sample |
|---|
| A two-component Family 2B encapsulin shell from Streptomyces lydicus with Encapsulin 1 enriched |
| Sample Components |
| Encapsulin 2 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 | 69590 |
| Reported Resolution (?) | 2.58 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Homogeneous refinement was performed against the ab-initio map with I symmetry, per-particle defocus optimization, per-group CTF parameterization, and ... |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (9BIX) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | correlation coefficient | ||||
| Overall B Value | 99.9 | ||||
| Fitting Procedure | |||||
| Details | The starting encapsulin model was first placed into the map using Chimera. It was then refined against the map by alternating rounds of manual refinem ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/?**2) | 45.5 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TALOS ARCTICA |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 1800 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 45000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | v3.2.0+210511 |
| IMAGE ACQUISITION | Leginon | |
| CTF CORRECTION | cryoSPARC | v3.2.0+210511 |
| MODEL FITTING | UCSF Chimera | v 1.15 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | v3.2.0+210511 |
| FINAL EULER ASSIGNMENT | cryoSPARC | v3.2.0+210511 |
| RECONSTRUCTION | cryoSPARC | v3.2.0+210511 |
| 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 | 77425 | |||
