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Symmetry relaxed reconstruction of Rhodospirillum rubrum encapsulin:encapsulated ferritin nanocompartment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 3.8896 f_angle_d 0.6995 f_chiral_restr 0.03 f_plane_restr 0.003 f_bond_d 0.0027
Sample Rhodospirillum rubrum encapsulin complex Sample Components Rhodospirillum rubrum encapsulated ferritin Rhodospirillum rubrum encapsulated ferritin localisation peptide
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 4 uL of sample was applied to the grids, which were then blotted
100% humidity blot force 5
wait time 10 s
blot time 3 seconds
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 41954 Reported Resolution (Å) 3.73 Resolution Method FSC 0.143 CUT-OFF Other Details Icosahedral reconstruction with symmetry relaxation by marginalization to reconstruct interior cargo density and encapculin shell. Refinement Type Symmetry Type POINT Point Symmetry I
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol OTHER Refinement Target Cross-correlation coefficient Overall B Value 33.7 Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS GLACIOS Minimum Defocus (nm) 600 Maximum Defocus (nm) 1600 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 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.7 MODEL REFINEMENT PHENIX 1.21.2_5419 CTF CORRECTION cryoSPARC 4.7 INITIAL EULER ASSIGNMENT cryoSPARC 4.7 FINAL EULER ASSIGNMENT cryoSPARC 4.7 CLASSIFICATION cryoSPARC 4.7 RECONSTRUCTION cryoSPARC 4.7
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 346315 Particles from icosahedral reconstruction of Encapsulin:Encapsulated Ferritin complex