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Cryo-EM structure of Rhodopsin-Gi bound to antibody fragment Fab13
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EN0 experimental model PDB 6CMO experimental model PDB 6CRK experimental model PDB 1GOT in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.659 f_angle_d 1.045 f_chiral_restr 0.048 f_bond_d 0.008 f_plane_restr 0.006
Sample Rhodopsin-Gi-Fab13 complex Sample Components Rhodopsin Guanine nucleotide-binding protein G(i) subunit alpha-1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 and Guanine nucleotide-binding protein G(T) subunit gamma-T1 Immunoglobin G light chain and Immunoglobin G heavy chain FAB fragment
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 587113 Reported Resolution (Å) 3.21 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (5EN0, 6CMO, 6CRK, 6CMO, 1GOT, 1GOT) Refinement Space REAL Refinement Protocol AB INITIO MODEL Refinement Target cross-correlation coefficient Overall B Value 150 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 66
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 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 3.31 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC MODEL FITTING UCSF Chimera 1.16 MODEL REFINEMENT PHENIX 1.20-4487
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 3752145