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Cryo-EM structure of the engineered vector AAV2.ATX002
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6U0R other Other
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.8988 f_angle_d 0.595 f_chiral_restr 0.0436 f_bond_d 0.0051 f_plane_restr 0.0042
Sample adeno-associated virus 2
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 14969 Reported Resolution (Å) 1.9 Resolution Method FSC 0.143 CUT-OFF Other Details Ewald sphere correction applied in RELION 5.0 Refinement Type Symmetry Type POINT Point Symmetry I
Map-Model Fitting and Refinement Id 1 (6U0R) 2 Refinement Space REAL Refinement Protocol FLEXIBLE FIT AB INITIO MODEL Refinement Target Cross-correlation Overall B Value Fitting Procedure Details Ab initio model created with ModelAngelo
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 30
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2000 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 165000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Topaz 0.3 IMAGE ACQUISITION EPU 3.7.1 CTF CORRECTION CTFFIND 4.1.14 MODEL FITTING UCSF ChimeraX 1.10.1 MODEL REFINEMENT PHENIX 1.21 INITIAL EULER ASSIGNMENT RELION 5.0 FINAL EULER ASSIGNMENT RELION 5.0 CLASSIFICATION RELION 5.0 RECONSTRUCTION RELION 5.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 160533