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Cryo-EM structure of the Arabidopsis thaliana CAT4 transporter in the outward-open L-ornithine bound state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q8W44K3-F1
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.7156 f_angle_d 0.5581 f_chiral_restr 0.0404 f_plane_restr 0.0038 f_bond_d 0.0024
Sample Complex of Arabidopsis thaliana cationic amino acid transporter 4 with a synthetic nanobody bound to L-ornithine, cholesterol and LMNG
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 76191 Reported Resolution (Å) 3.32 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (9HJK) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target cross-correlation coefficient Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2000 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.4 MODEL REFINEMENT PHENIX 1.21_5207 CLASSIFICATION cryoSPARC 4.7.1 RECONSTRUCTION cryoSPARC 4.7.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION