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Klebsiella pneumoniae DyP peroxidase-loaded encapsulin shell
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BOJ
Sample Klebsiella pneumoniae DyP peroxidase-loaded encapsulin shell Sample Components Klebsiella pneumoniae family 1 encapsulin shell Klebsiella pneumoniae encapsulated DyP peroxidase
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Blot force: 20
Blot time: 4 seconds
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 64969 Reported Resolution (Å) 2.52 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry I
Map-Model Fitting and Refinement Id 1 (7BOJ) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Cross-correlation coefficient Overall B Value 95.2 Fitting Procedure Details Initial fitting was performed using ChimeraX v1.2.5. The model was then manually refined and mutated using Coot v9.8.1 followed by real-space refineme ... Initial fitting was performed using ChimeraX v1.2.5. The model was then manually refined and mutated using Coot v9.8.1 followed by real-space refinement using Phenix v1.20.1-4487-000.
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 41.67
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA Minimum Defocus (nm) 800 Maximum Defocus (nm) 1800 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 45000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.2.1 IMAGE ACQUISITION Leginon CTF CORRECTION cryoSPARC 4.2.1 MODEL FITTING UCSF ChimeraX 1.2.5 MODEL FITTING Coot 0.9.8 MODEL REFINEMENT PHENIX 1.20.1-4487-000 INITIAL EULER ASSIGNMENT cryoSPARC 4.2.1 FINAL EULER ASSIGNMENT cryoSPARC 4.2.1 RECONSTRUCTION cryoSPARC 4.2.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 75967