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Cryo-EM structure of hydroxychloroquine-bound 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 17.907 r_dihedral_angle_6_deg 16.9 r_dihedral_angle_1_deg 4.036 r_angle_refined_deg 1.361 r_angle_other_deg 0.904 r_dihedral_angle_2_deg 0.559 r_nbd_refined 0.233 r_symmetry_nbd_other 0.221 r_nbtor_refined 0.211 r_xyhbond_nbd_refined 0.157
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.907 r_dihedral_angle_6_deg 16.9 r_dihedral_angle_1_deg 4.036 r_angle_refined_deg 1.361 r_angle_other_deg 0.904 r_dihedral_angle_2_deg 0.559 r_nbd_refined 0.233 r_symmetry_nbd_other 0.221 r_nbtor_refined 0.211 r_xyhbond_nbd_refined 0.157 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.054 r_gen_planes_other 0.011 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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:Nb3.7:hydroxychloroquine 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 249857 Reported Resolution (Å) 3 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 FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 58
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 2700 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 215000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC IMAGE ACQUISITION SerialEM 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