6WCQ
Structure of a substrate-bound DQC ubiquitin ligase
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 11.807 |
| f_angle_d | 0.562 |
| f_chiral_restr | 0.038 |
| f_plane_restr | 0.003 |
| f_bond_d | 0.002 |
| Sample |
|---|
| CUL1-SKP1-FBXL17-KEAP1 complex |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE-PROPANE |
| Sample Vitrification Details | |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE-PROPANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 160256 |
| Reported Resolution (Å) | 8.5 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1LDK, 1X1X) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Coordinates were fitted as rigid bodies or fragments in Chimera and subsequently geometry-optimized using PHENIX real space refinement. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | GATAN K2 SUMMIT (4k x 4k) | |||||||
| Electron Dose (electrons/Å**2) | 60 | 50 | |||||||
| Imaging Experiment | 1 | 2 |
|---|---|---|
| Date of Experiment | ||
| Temperature (Kelvin) | ||
| Microscope Model | FEI TALOS ARCTICA | FEI TALOS ARCTICA |
| Minimum Defocus (nm) | 2000 | 1500 |
| Maximum Defocus (nm) | 3000 | 3000 |
| Minimum Tilt Angle (degrees) | ||
| Maximum Tilt Angle (degrees) | ||
| Nominal CS | 2.7 | 2.7 |
| Imaging Mode | BRIGHT FIELD | BRIGHT FIELD |
| Specimen Holder Model | OTHER | OTHER |
| Nominal Magnification | ||
| Calibrated Magnification | ||
| Source | FIELD EMISSION GUN | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | CTFFIND | 4 |
| CTF CORRECTION | Gctf | |
| MODEL FITTING | UCSF Chimera | |
| IMAGE ACQUISITION | SerialEM | |
| INITIAL EULER ASSIGNMENT | RELION | 3 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | |
| FINAL EULER ASSIGNMENT | RELION | 3 |
| RECONSTRUCTION | RELION | 3 |
| MODEL REFINEMENT | PHENIX | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | As implemented in RELION. | 824561 | Total number of particles for both datasets. Selected using RELION auto-picking (Laplacian-of-Gaussian). | |
