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Neck of phage 812 virion (C6)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold in silico model Other
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.056 f_angle_d 0.522 f_chiral_restr 0.044 f_bond_d 0.004 f_plane_restr 0.004
Sample Staphylococcus phage 812
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 21731 Reported Resolution (Å) 4.15 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C6
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol AB INITIO MODEL Refinement Target cross-correlation coefficient Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON II (4k x 4k) Electron Dose (electrons/Å**2) 49
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1200 Maximum Defocus (nm) 2400 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 75000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION EMAN2 IMAGE ACQUISITION EPU CTF CORRECTION Gctf 1.0.6 MODEL FITTING Coot 0.9 MODEL REFINEMENT PHENIX 1.19 MODEL REFINEMENT ISOLDE 1.4 INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 23947 Manual particle selection