8TNQ
Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 1
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 4.1904 |
| f_angle_d | 0.5006 |
| f_chiral_restr | 0.0437 |
| f_plane_restr | 0.0053 |
| f_bond_d | 0.0042 |
| Sample |
|---|
| Ternary Complex of DDB1dB:CRBN:PT-179 with SD40 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | LEICA EM GP |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic ... |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 289691 |
| Reported Resolution (Å) | 2.41 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (8G46, 5FQD, 6H0F) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | 70 | ||||
| Fitting Procedure | |||||
| Details | Phenix real-space refinement without rigid body, with ADP. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 52 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 2000 |
| 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 | 4.2.0 |
| MODEL FITTING | UCSF ChimeraX | 1.6.1 |
| MODEL REFINEMENT | PHENIX | 1.20.1 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.2.0 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.2.0 |
| CLASSIFICATION | RELION | 4.0.1 |
| RECONSTRUCTION | cryoSPARC | 4.2.0 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 6798113 | |||
