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Cryo-EM structure of MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 33CG
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.748 f_angle_d 0.556 f_chiral_restr 0.043 f_plane_restr 0.004 f_bond_d 0.003
Sample MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-6
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 349805 Reported Resolution (Å) 2.4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (33CG, 33CG, 33CG, 33CG, 33CG) Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC PARTICLE SELECTION Topaz CTF CORRECTION cryoSPARC MODEL FITTING ISOLDE MODEL FITTING Coot INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC 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 2403407