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Focused refinement of closed pentamer of the Rhodospirillum rubrum encapsulin from symmetry expansion of icosahedral single particle reconstruction
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 4.0115 f_angle_d 0.5216 f_chiral_restr 0.0395 f_plane_restr 0.0035 f_bond_d 0.0027
Sample Rhodospirillum rubrum encapsulin
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details blot force 5, wait time 10 s, and blot time 3 seconds
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 2299907 Reported Resolution (Å) 2.17 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol AB INITIO MODEL Refinement Target Cross correlation Overall B Value 70 Fitting Procedure Details Real space refinement in phenix
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 42
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS 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) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.7 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.7 MODEL FITTING UCSF ChimeraX 1.10 MODEL REFINEMENT PHENIX 1.21.2_5419 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 3438531 Blob picker