☰ Navigation Tabs
Mycoplasma pneumoniae large ribosomal subunit in chloramphenicol-treated cells
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OOD experimental model PDB 7OOC
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.159 f_angle_d 0.597 f_chiral_restr 0.029 f_plane_restr 0.005 f_bond_d 0.004
Sample Large ribosomal subunit with some elements of the small ribosomal subunit. Focused refinement on 50S subunit of the in situ 70S subunit map.
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 control chamber.
3D Reconstruction Reconstruction Method SUBTOMOGRAM AVERAGING Number of Particles 30774 Reported Resolution (Å) 2.9 Resolution Method FSC 0.143 CUT-OFF Other Details half maps from Warp/M Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7OOD, 7OOC) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Cross-correlation coefficient Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 3.34
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 3250 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 64000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version VOLUME SELECTION PyTom 0.9.7.1 VOLUME SELECTION Warp 1.0.9 IMAGE ACQUISITION SerialEM 3.9 CTF CORRECTION Warp 1.0.9 MODEL FITTING Coot 0.9.6 MODEL FITTING Coot 0.9.8.5 MODEL FITTING CCP4 package 8.0 FINAL EULER ASSIGNMENT RELION 3.0.8 FINAL EULER ASSIGNMENT Warp 1.0.9 CLASSIFICATION RELION 3.0.8 RECONSTRUCTION Warp 1.0.9 MODEL REFINEMENT PHENIX 1.20.1_4487
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION CTF estimation and 3D CTF correction are done in Warp