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Cryo-EM structure of HLA-B*73:01 bound to a 9mer peptide and two Fabs
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8TMU in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.585 f_angle_d 0.485 f_chiral_restr 0.042 f_plane_restr 0.004 f_bond_d 0.003
Sample Ternary complex of B.1 and B.8 Fabs with single-chain P2R-B2M-HLA-B*73:01
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 502247 Reported Resolution (Å) 3.1 Resolution Method FSC 0.143 CUT-OFF Other Details Masked Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (8TMU) Refinement Space REAL Refinement Protocol AB INITIO MODEL Refinement Target EMRinger Overall B Value 86.65 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2400 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 81000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU MODEL FITTING UCSF ChimeraX 1.5 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