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Cryo-EM structure of ADP-bound Vientovirus FB Rep hexamer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9PQJ
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.588 f_angle_d 0.633 f_chiral_restr 0.041 f_plane_restr 0.004 f_bond_d 0.002
Sample ADP-bound Vientovirus FB Rep hexamer
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 312272 Reported Resolution (Å) 3.2 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (9PQJ) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value 99.33 Fitting Procedure Details Initial rigid body fitting in ChimeraX and then Coot for flexible fitting
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 42.2
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 3000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.5.3 PARTICLE SELECTION cryoSPARC 4.5.3 PARTICLE SELECTION Topaz 0.2.4 CTF CORRECTION cryoSPARC 4.5.3 CTF CORRECTION RELION 5.0-beta MODEL FITTING UCSF ChimeraX 1.9 MODEL FITTING Coot 0.9.8.96 INITIAL EULER ASSIGNMENT cryoSPARC 4.5.3 FINAL EULER ASSIGNMENT RELION 5.0-beta CLASSIFICATION RELION 5.0-beta RECONSTRUCTION RELION 5.0-beta MODEL REFINEMENT PHENIX 1.21_5207
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 4802310