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Cryo-EM structure of bovine concentrative nucleoside transporter 3 in complex with N-hydroxycytidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TIJ
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.441 f_angle_d 0.425 f_chiral_restr 0.035 f_plane_restr 0.003 f_bond_d 0.002
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 147332 Reported Resolution (Å) 2.74 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C3
Map-Model Fitting and Refinement Id 1 (3TIJ) 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) 1000 Maximum Defocus (nm) 2250 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 81000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 3.3 IMAGE ACQUISITION Latitude 3.5 CTF CORRECTION CTFFIND 4 MODEL FITTING Coot 0.96 MODEL REFINEMENT PHENIX 1.18 INITIAL EULER ASSIGNMENT cryoSPARC 3.3 FINAL EULER ASSIGNMENT cryoSPARC 3.3 CLASSIFICATION cryoSPARC 3.3 RECONSTRUCTION cryoSPARC 3.3
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING ONLY 1687435