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Acheta domesticus segmented densovirus, mature virion capsid structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UX1
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.919 f_angle_d 0.836 f_chiral_restr 0.056 f_bond_d 0.01 f_plane_restr 0.006
Sample unclassified Densovirinae
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 150469 Reported Resolution (Å) 2.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry I
Map-Model Fitting and Refinement Id 1 (3UX1) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 75
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 650 Maximum Defocus (nm) 4000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode OTHER Specimen Holder Model Nominal Magnification Calibrated Magnification Source OTHER Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cisTEM 1.0.0 CTF CORRECTION CTFFIND 4 MODEL FITTING UCSF Chimera 1.13.1 FINAL EULER ASSIGNMENT cisTEM 1.0.0 CLASSIFICATION cisTEM 1.0.0 RECONSTRUCTION cisTEM 1.0.0 MODEL REFINEMENT Coot 0.8.9.3 MODEL REFINEMENT PHENIX 1.20.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING ONLY 188074