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cryoEM structure of Escherichia phage YDC107 tail core
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.6535 f_angle_d 0.6663 f_chiral_restr 0.0428 f_plane_restr 0.0049 f_bond_d 0.0035
Sample Escherichia phage YDC107_1
Specimen Preparation Sample Aggregation State FILAMENT Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details blot force 1
blot time 6.5 s
3D Reconstruction Reconstruction Method HELICAL Number of Particles 5927 Reported Resolution (Å) 3.22 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type HELICAL Axial Symmetry C6 Axial Rise 41.77 Angular Rotation 17.9
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 54
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 81000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION Leginon CTF CORRECTION cryoSPARC MODEL FITTING UCSF Chimera INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC 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