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Cryo-EM structure of apo human SLC19A3 in inward-open state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.734 r_dihedral_angle_6_deg 16.829 r_dihedral_angle_1_deg 3.957 r_angle_refined_deg 1.324 r_angle_other_deg 0.681 r_dihedral_angle_2_deg 0.595 r_nbd_refined 0.219 r_symmetry_nbd_other 0.218 r_nbtor_refined 0.205 r_xyhbond_nbd_refined 0.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.734 r_dihedral_angle_6_deg 16.829 r_dihedral_angle_1_deg 3.957 r_angle_refined_deg 1.324 r_angle_other_deg 0.681 r_dihedral_angle_2_deg 0.595 r_nbd_refined 0.219 r_symmetry_nbd_other 0.218 r_nbtor_refined 0.205 r_xyhbond_nbd_refined 0.199 r_symmetry_xyhbond_nbd_other 0.116 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.055 r_gen_planes_other 0.011 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_lrange_it r_lrange_other
Sample SLC19A3:Nb3.3-apo Sample Components SLC19A3 Nb3.3
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 512258 Reported Resolution (Å) 2.87 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol AB INITIO MODEL Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 45
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 1600 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC MODEL FITTING ISOLDE MODEL REFINEMENT PHENIX INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION