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Human sodium-dependent vitamin C transporter 1 bound to L-ascorbic acid in an inward-open state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Q9UHI7
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.054 r_long_range_B_refined 21.498 r_long_range_B_other 21.497 r_dihedral_angle_4_deg 17.845 r_dihedral_angle_3_deg 15.801 r_scangle_other 12.111 r_mcangle_it 8.766 r_mcangle_other 8.765 r_scbond_it 7.717 r_scbond_other 7.715
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.054 r_long_range_B_refined 21.498 r_long_range_B_other 21.497 r_dihedral_angle_4_deg 17.845 r_dihedral_angle_3_deg 15.801 r_scangle_other 12.111 r_mcangle_it 8.766 r_mcangle_other 8.765 r_scbond_it 7.717 r_scbond_other 7.715 r_mcbond_it 6.193 r_mcbond_other 6.191 r_dihedral_angle_1_deg 5.14 r_angle_refined_deg 1.545 r_angle_other_deg 1.502 r_chiral_restr 0.1 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_gen_planes_other 0.009 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Sample Human SVCT1 dimer in a substrate-bound inward-open state
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 147401 Reported Resolution (Å) 2.49 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 49.7
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 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 RELION 3.1.1 IMAGE ACQUISITION SerialEM 3.9.0 CTF CORRECTION RELION 3.1.1 MODEL FITTING Coot 0.9.6 MODEL REFINEMENT Servalcat 0.2.115 INITIAL EULER ASSIGNMENT RELION 3.1.1 FINAL EULER ASSIGNMENT RELION 3.1.1 CLASSIFICATION RELION 3.1.1 RECONSTRUCTION RELION 3.1.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2852953