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ASCT2 trimer in lipid nanodiscs with bound glutamine and Na+ ions in the outward-facing state (OFS)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MPB
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 3.769 f_angle_d 0.486 f_chiral_restr 0.036 f_plane_restr 0.005 f_bond_d 0.003
Sample ASCT2 in MSP2N2 lipid nanodiscs with glutamine and Na+ ions
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE-PROPANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 980802 Reported Resolution (Å) 2.6 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C3
Map-Model Fitting and Refinement Id 1 (6MPB) Refinement Space REAL Refinement Protocol FLEXIBLE 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 FEI TITAN KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 2900 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 59809 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION crYOLO 1.7.6 IMAGE ACQUISITION EPU 2.10 CTF CORRECTION CTFFIND 4.1.14 MODEL FITTING Coot 0.9.6 MODEL FITTING ISOLDE 1.6.0 MODEL REFINEMENT PHENIX 1.20.1 INITIAL EULER ASSIGNMENT RELION 3.1.0 FINAL EULER ASSIGNMENT RELION 3.1.0 RECONSTRUCTION RELION 3.1.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 7639781