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Cryo-EM structure of trimeric human STEAP1 bound to three Fab120.545 fragments
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.