8U4Z
Klebsiella pneumoniae encapsulin-associated DyP peroxidase
ELECTRON MICROSCOPY
| Sample |
|---|
| Klebsiella pneumoniae family 1 encapsulin-associated DyP peroxidase |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Blot force: 5 Blot time: 2 seconds |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 431317 |
| Reported Resolution (Å) | 2.39 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Unmasked local refinement was performed with D3 symmetry imposed. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | D3 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | 107.7 | ||||
| Fitting Procedure | |||||
| Details | Initial fitting was performed using ChimeraX v1.2.5. The model was then manually refined and mutated using Coot v9.8.1 followed by real-space refineme ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 50.02 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 1800 |
| 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 | 4.4.0+231114 |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | cryoSPARC | 4.4.0+231114 |
| MODEL FITTING | UCSF ChimeraX | 1.2.5 |
| MODEL FITTING | Coot | 0.9.8 |
| MODEL REFINEMENT | PHENIX | 1.20.1-4487-000 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.4.0+231114 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.4.0+231114 |
| RECONSTRUCTION | cryoSPARC | 4.4.0+231114 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 2603020 | |||
