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Structural characterization of hibernating ribosomes in the Gram-negative pathogen Enterobacter cloacae complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BOX
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 22.403 f_angle_d 0.6465 f_chiral_restr 0.0401 f_bond_d 0.0058 f_plane_restr 0.0057
Sample Enterobacter hormaechei subsp. Xiangfangensis Ribosome
Specimen Preparation Sample Aggregation State CELL Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 87433 Reported Resolution (Å) 2.8 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (8B0X) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details Rigid body fitting of each separate chain in chimera, followed by manual adjustment and point mutation in coot.
Final refinement in Phenix minimizatio ... Rigid body fitting of each separate chain in chimera, followed by manual adjustment and point mutation in coot.
Final refinement in Phenix minimization_global 5 macro cycles
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 35
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2500 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 81000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.3.1 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.3.1 MODEL FITTING UCSF Chimera 1.18 MODEL FITTING Coot 0.9.8.95 INITIAL EULER ASSIGNMENT cryoSPARC 4.3.1 FINAL EULER ASSIGNMENT cryoSPARC 4.3.1 CLASSIFICATION cryoSPARC 4.3.1 RECONSTRUCTION cryoSPARC 4.3.1 RECONSTRUCTION PHENIX 1.21.2-5419 RECONSTRUCTION Coot 0.9.8.95 MODEL REFINEMENT PHENIX 1.21.2-5419
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1508999