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Structural characterization of hibernating ribosomes in the Gram-negative pathogen Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7UNW
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 22.8564 f_angle_d 0.7539 f_chiral_restr 0.0469 f_bond_d 0.0075 f_plane_restr 0.0064
Sample Pseudomonas aeruginosa PA14 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 131785 Reported Resolution (Å) 2.6 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7UNW) 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 Coot 0.9.8.95 MODEL FITTING UCSF Chimera 1.18 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 Coot 0.9.8.95 RECONSTRUCTION UCSF Chimera 1.18 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 3030492