ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 6.144 |
| f_angle_d | 0.92 |
| f_chiral_restr | 0.059 |
| f_plane_restr | 0.008 |
| f_bond_d | 0.007 |
| Sample |
|---|
| Lon protease bound to Y2853 substrate |
| 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 | 118143 |
| Reported Resolution (Å) | 3 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Focused classification of final reconstruction was performed on E and F "step" subunits, resulting in a reconstruction with an overall resolution of 3 ... |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | AB INITIO MODEL | ||||
| Refinement Target | Correlation coefficient | ||||
| Overall B Value | 52 | ||||
| Fitting Procedure | |||||
| Details | Initial homology model was built using SWISS-MODEL and initial rigid body docking was done using UCSF Chimera | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 52 | ||||||||
| 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 |
| PARTICLE SELECTION | FindEM | 1 |
| IMAGE ACQUISITION | Leginon | 3.0 |
| CTF CORRECTION | RELION | 2.0b |
| MODEL FITTING | Coot | 0.8.8 |
| INITIAL EULER ASSIGNMENT | RELION | 2.0b |
| FINAL EULER ASSIGNMENT | RELION | 2.0b |
| CLASSIFICATION | RELION | 2.0b |
| RECONSTRUCTION | RELION | 2.0b |
| 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 RELION | 1176206 | template-based cross correlation with FindEM | |
