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Cryo-EM ternary structure of CD1c presenting a mycobacterial lipid to a T cell receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model SwissModel experimental model PDB 6C15
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.452 f_angle_d 0.635 f_chiral_restr 0.047 f_plane_restr 0.006 f_bond_d 0.004
Sample Ternary complex of CD1c presenting mycobacterial phosphomycoketide lipid to the MPM7 alpha-beta T cell receptor Sample Components CD1c and beta-2-microglobulin heterodimer MPM7 alpha-beta T cell receptor
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 130855 Reported Resolution (Å) 2.9 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (6C15, 6C15) Refinement Space Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 1500 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 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4 PARTICLE SELECTION Topaz CTF CORRECTION cryoSPARC 4 MODEL FITTING PHENIX 1.21.2_5419 INITIAL EULER ASSIGNMENT cryoSPARC 4 FINAL EULER ASSIGNMENT cryoSPARC 4 CLASSIFICATION cryoSPARC 4 RECONSTRUCTION cryoSPARC MODEL REFINEMENT PHENIX 1.21.2_5419 MODEL REFINEMENT Servalcat
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION