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Structure of human excitatory amino acid transporter 3 (EAAT3) in complex with B11 nanobody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6S3Q experimental model PDB 1ZVH
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.752 f_angle_d 0.4678 f_chiral_restr 0.0384 f_plane_restr 0.0037 f_bond_d 0.0023
Sample human excitatory amino acid transporter 3 (EAAT3) in complex with B11 nanobody
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 132709 Reported Resolution (Å) 3.5 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6S3Q, 1ZVH) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target real space refinement Overall B Value Fitting Procedure Details initial model fitted with 6S3Q for EAAT3 and 1ZVH for B11 nanobody in COOT. Model was refined in Phenix.
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 38.55
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2400 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 FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details Objective aperture 100 um; data collected on eBIC-Diamond Krios III microscope
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 3.3.1 CTF CORRECTION cryoSPARC 3.3.1 MODEL FITTING Coot 0.9.8.93 INITIAL EULER ASSIGNMENT cryoSPARC 3.3.1 FINAL EULER ASSIGNMENT cryoSPARC 3.3.1 CLASSIFICATION cryoSPARC 3.3.1 RECONSTRUCTION cryoSPARC 3.3.1 MODEL REFINEMENT PHENIX 1.21.1_5286
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION