ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| in silico model | AlphaFold | ||
| experimental model | PDB | 4V3L | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 4.317 |
| f_angle_d | 0.445 |
| f_chiral_restr | 0.036 |
| f_plane_restr | 0.003 |
| f_bond_d | 0.002 |
| Sample |
|---|
| Ternary complex of E3 ubiquitin ligase Tom1 with E2 ubiquitin conjugating enzyme UBE2D2 and ubiquitin |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | LEICA EM GP |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | CHAPSO detergent added to final conc. of 0.2 mM. Sample applied twice. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 246341 |
| Reported Resolution (Å) | 2.8 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (4V3L, 4V3L) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | 89.6 | ||||
| Fitting Procedure | |||||
| Details | Phenix real-space refinement | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 56.13 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 2200 |
| 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 | 105000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | Topaz | 0.2.5 |
| IMAGE ACQUISITION | SerialEM | 4.1b |
| CTF CORRECTION | cryoSPARC | 4.4.1 |
| MODEL FITTING | UCSF ChimeraX | 1.6.1 |
| MODEL FITTING | ISOLDE | 1.6.0 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.4.1 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.4.1 |
| CLASSIFICATION | cryoSPARC | 4.4.1 |
| RECONSTRUCTION | cryoSPARC | 4.4.1 |
| MODEL REFINEMENT | PHENIX | 1.19.2-4158 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 11388836 | Initial 2D classes assisted template picking in cryoSPARC Live. | ||
