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Single particle reconstruction of Rhodospirillum rubrum encapsulated ferritin in encapsulin nano compartment
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 3.6201 f_angle_d 0.7657 f_chiral_restr 0.0398 f_bond_d 0.0048 f_plane_restr 0.0038
Sample Encapsulated ferritin decamer
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 272846 Reported Resolution (Å) 2.79 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry D5
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol AB INITIO MODEL Refinement Target Overall B Value Fitting Procedure Details Ab intio model produced in ModelAngelo
Refined in Phenix.realspace refine
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 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 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.7 INITIAL EULER ASSIGNMENT cryoSPARC 4.6 FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION cryoSPARC 4.6 RECONSTRUCTION cryoSPARC 4.7 MODEL REFINEMENT PHENIX 2.1_6048
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 272846 Particles from sub-particle selection