8OV6
Ternary structure of intramolecular bivalent glue degrader IBG1 bound to BRD4 and DCAF16:DDB1deltaBPB
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 4.9386 |
| f_angle_d | 0.5047 |
| f_chiral_restr | 0.0418 |
| f_plane_restr | 0.0042 |
| f_bond_d | 0.0025 |
| Sample |
|---|
| Ternary complex of bivalent glue degrader compound 1 bound to BRD4 and DCAF16:DDB1deltaBPB |
| Sample Components |
| DCAF16:DDB1deltaBPB E3 ligase substrate receptor:apator complex |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 3.5 uL complex was dispensed onto the grid, allowed to disperse for 10 s, blotted for 3.5 s using blot force 3, then plunged into liquid ethane |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 192014 |
| Reported Resolution (Å) | 3.77 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (5FQD, 3MXF, 6DUV) | ||||
| Refinement Space | |||||
| Refinement Protocol | |||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | TFS FALCON 4i (4k x 4x) | ||||||||
| Electron Dose (electrons/Å**2) | 12.7 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS GLACIOS |
| Minimum Defocus (nm) | 1700 |
| Maximum Defocus (nm) | 3200 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 190000 |
| Calibrated Magnification | 190000 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 4.1.2 |
| IMAGE ACQUISITION | EPU | 3.0 |
| CTF CORRECTION | cryoSPARC | 4.1.2 |
| MODEL FITTING | PHENIX | 1.20.1-4487 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.1.2 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.2.1 |
| RECONSTRUCTION | cryoSPARC | |
| MODEL REFINEMENT | PHENIX | 1.20.1-4487 |
| MODEL REFINEMENT | UCSF ChimeraX | 1.6.dev202302040126 |
| MODEL REFINEMENT | ISOLDE | 1.6.dev1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||
