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high-affinity choline transporter in DDM with Na+ and choline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 3.295 f_angle_d 0.49 f_chiral_restr 0.037 f_plane_restr 0.003 f_bond_d 0.002
Sample high-affinity choline transporter in DDM with Na+ and choline
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 447418 Reported Resolution (Å) 3.28 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value 53.4 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOCONTINUUM (6k x 4k) Electron Dose (electrons/Å**2) 59.8
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 1600 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 130000 Calibrated Magnification Source LAB6 Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC v4.4 PARTICLE SELECTION Topaz IMAGE ACQUISITION EPU 3.8.0.7600 CTF CORRECTION cryoSPARC v4.4 MODEL FITTING UCSF ChimeraX 1.6rc202304202331 INITIAL EULER ASSIGNMENT cryoSPARC v4.4 FINAL EULER ASSIGNMENT cryoSPARC v4.4 CLASSIFICATION cryoSPARC v4.4 RECONSTRUCTION cryoSPARC v4.4 MODEL REFINEMENT PHENIX 1.21.1_5286 MODEL REFINEMENT Coot 0.9.4.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION