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E. coli plasmid-borne JetABCD(E248A) core in a cleavage-competent state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8AS8 in silico model AlphaFold in silico model Other
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.485 f_angle_d 0.551 f_chiral_restr 0.037 f_plane_restr 0.004 f_bond_d 0.003
Sample JetABCD(E248A) loaded onto plasmid DNA
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 235956 Reported Resolution (Å) 4.17 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 (8AS8) Refinement Space Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2600 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 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 3.3 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.1 MODEL FITTING ISOLDE MODEL FITTING Coot MODEL FITTING UCSF ChimeraX MODEL REFINEMENT PHENIX 1.20.1_4487: RECONSTRUCTION cryoSPARC 3.3
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION