Cryo-EM structure of KBTBD4 WT-HDAC2 2:1 complex mediated by molecular glue UM171
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 7ZZT | |
| in silico model | AlphaFold | AF-Q9N010-F1 | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 6.247 |
| f_angle_d | 0.816 |
| f_chiral_restr | 0.048 |
| f_bond_d | 0.007 |
| f_plane_restr | 0.006 |
| Sample |
|---|
| KBTBD4 WT-HDAC2 2:1 complex mediated by molecular glue UM171 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 264324 |
| Reported Resolution (Å) | 3.13 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (7ZZT) | ||||
| Refinement Space | |||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | |||||
| Overall B Value | 123.7 | ||||
| Fitting Procedure | |||||
| Details | Initial local fitting was done using Chimera. Then WinCoot and Phenix was used for model refinement and validation. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 38 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 3200 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 105000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL REFINEMENT | PHENIX | 1.20.1_4487: |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 13588054 | |||
