6V11
Lon Protease from Yersinia pestis
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6ON2 | |
| Sample |
|---|
| Lon Protease from Yersinia pestis |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | HOMEMADE PLUNGER |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 4 uL of sample was applied per grid and manually blotted for 4 seconds followed by immediately plunge-freezing in liquid ethane cooled by liquid nitro ... |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 140506 |
| Reported Resolution (Å) | 3.8 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6ON2) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Correlation coefficient | ||||
| Overall B Value | 115 | ||||
| Fitting Procedure | |||||
| Details | Initial rigid body docking was done using UCSF Chimera | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 50 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TALOS ARCTICA |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 1200 |
| 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 | Coma-free alignment procedure from Herzik & Wu, Nature Methods (2017). Preliminary grid screening was performed manually prior to data collection. |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | Leginon | 3.0 |
| CTF CORRECTION | Warp | 1.0.7 |
| MODEL FITTING | Coot | 0.8.8 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 2.11.0 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 2.11.0 |
| CLASSIFICATION | cryoSPARC | 2.11.0 |
| RECONSTRUCTION | cryoSPARC | 2.11.0 |
| MODEL REFINEMENT | PHENIX | 1.11.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING ONLY | CTF correction in Warp | 412719 | Particles were selected from a subset of micrographs using BoxNet automated particle picker | |
