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70S ribosome with EF-Tu-tRNA and P-site tRNA in pseudouridimycin-treated Mycoplasma pneumoniae cells
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OOC experimental model PDB 7OOD experimental model PDB 4V7C experimental model PDB 4V5L
Sample Cryo-electron tomograms of pseudouridimycin-treated Mycoplasma pneumoniae cells
Specimen Preparation Sample Aggregation State CELL Vitrification Instrument HOMEMADE PLUNGER Cryogen Name ETHANE-PROPANE Sample Vitrification Details back-side blotting for 2-3 seconds before plunging using a manual plunger without an environmental chamber
3D Reconstruction Reconstruction Method SUBTOMOGRAM AVERAGING Number of Particles 1128 Reported Resolution (Å) 9.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7OOC, 7OOD, 4V7C, 4V7C, 4V5L) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 3.2
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1500 Maximum Defocus (nm) 3750 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 VOLUME SELECTION PyTom VOLUME SELECTION Warp 3.0.7 beta or 3.0.9 IMAGE ACQUISITION SerialEM CTF CORRECTION RELION 3.0.8 MODEL FITTING PHENIX 1.18 FINAL EULER ASSIGNMENT RELION 3.0.8 CLASSIFICATION RELION 3.0.8 RECONSTRUCTION RELION 3.0.8 MODEL REFINEMENT PHENIX 1.18
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION