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WT strain gidB mutant mycobacterial ribosome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5O60 experimental model PDB 5O5J
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.089 f_angle_d 0.652 f_chiral_restr 0.04 f_plane_restr 0.006 f_bond_d 0.004
Sample Mycobacterium smegmatis ribosome, WT strain, gidB mutant
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 1466881 Reported Resolution (Å) 2.47 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (5o60, 5o5j) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 901.165
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 1500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cisTEM development IMAGE ACQUISITION SerialEM CTF CORRECTION cisTEM development MODEL FITTING UCSF ChimeraX MODEL FITTING ISOLDE MODEL FITTING Coot MODEL FITTING PyMOL MODEL REFINEMENT PHENIX 1.19.2_4158 MODEL REFINEMENT ISOLDE INITIAL EULER ASSIGNMENT cisTEM development FINAL EULER ASSIGNMENT cisTEM development CLASSIFICATION cisTEM development RECONSTRUCTION cisTEM development
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION