6Y9B
Cryo-EM structure of trimeric human STEAP1 bound to three Fab120.545 fragments
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6HCY | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 17.684 |
| f_angle_d | 0.526 |
| f_chiral_restr | 0.042 |
| f_bond_d | 0.004 |
| f_plane_restr | 0.003 |
| Sample |
|---|
| Trimeric human six-transmembrane epithelial antigen of the prostate (STEAP1) bound to three Fab-fragments of antibody mAb120.545 |
| Sample Components |
| Fab-fragment 1 of antibody mAb120.545 |
| Homo-trimeric STEAP1, chain a, b and c. |
| Fab Fragment 2 of antibody mAb120.545 |
| Fab-fragment 3 of antibody mAb120.545 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE-PROPANE |
| Sample Vitrification Details | blot 4 seconds, blotforce 0 |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 169426 |
| Reported Resolution (Å) | 2.97 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Final reconstruction was generated in Relion. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C3 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6HCY) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | 100.9 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 49.5 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TALOS ARCTICA |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 3000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 130000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details | Data was collected on a 200 kV Talos Arctica, located at Utrecht University, the Netherlands. |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | Gctf | 1.18 |
| MODEL FITTING | UCSF Chimera | 1.12 |
| INITIAL EULER ASSIGNMENT | RELION | 3.0 |
| FINAL EULER ASSIGNMENT | RELION | 3.1beta |
| CLASSIFICATION | RELION | 3.1beta |
| RECONSTRUCTION | RELION | 3.1beta |
| MODEL REFINEMENT | PHENIX | 1.17.1-3660 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 616302 | Picking was performed in Relion. | ||
