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Turnip Crinkle Virus: virions (TCV-M)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9QVF
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 3.437 f_angle_d 0.423 f_chiral_restr 0.04 f_plane_restr 0.003 f_bond_d 0.002
Sample Turnip crinkle virus
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 9981 Reported Resolution (Å) 3.43 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry I
Map-Model Fitting and Refinement Id 1 (9QVF) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target cross-correlation coefficient Overall B Value 83 Fitting Procedure Details
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 30
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS TALOS F200C Minimum Defocus (nm) 700 Maximum Defocus (nm) 2100 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model GATAN ELSA 698 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Nominal Magnification 150000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.5.3 IMAGE ACQUISITION EPU 3.7.1.6940 CTF CORRECTION cryoSPARC 4.5.3 MODEL FITTING UCSF ChimeraX 1.8 MODEL FITTING Coot 0.9.8.95 EL (ccp4) INITIAL EULER ASSIGNMENT cryoSPARC 4.5.3 FINAL EULER ASSIGNMENT cryoSPARC 4.5.3 CLASSIFICATION cryoSPARC 4.5.3 RECONSTRUCTION cryoSPARC 4.5.3 MODEL REFINEMENT PHENIX 1.21.2_5419
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 22567