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Mature 50S ribosomal subunit from RrmJ knock out E.coli strain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YBB experimental model PDB 5H5U
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.875 f_angle_d 0.718 f_chiral_restr 0.043 f_bond_d 0.007 f_plane_restr 0.005
Sample Mature 50S ribosomal subunit from RrmJ knock out E.coli strain
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details blot for 2 seconds before plunging
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 98194 Reported Resolution (Å) 3.14 Resolution Method FSC 0.143 CUT-OFF Other Details A soft mask was added to improve resolution at the final refinement. Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (4YBB, 5H5U) 2 (4YBB, 5H5U) Refinement Space RECIPROCAL Refinement Protocol RIGID BODY FIT Refinement Target Correlation coefficient Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON II (4k x 4k) Electron Dose (electrons/Å**2) 45
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) -1000 Maximum Defocus (nm) -2000 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 75000 Calibrated Magnification 75000 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details Preliminary grid screening was performed manually.
EM Software Task Software Package Version PARTICLE SELECTION RELION 1.4 CTF CORRECTION CTFFIND 3.0 MODEL FITTING UCSF Chimera 1.13 INITIAL EULER ASSIGNMENT RELION 1.4 FINAL EULER ASSIGNMENT RELION 1.4 CLASSIFICATION RELION 1.4 RECONSTRUCTION RELION 1.4 MODEL REFINEMENT PHENIX 1.16 MODEL REFINEMENT REFMAC 5 MODEL FITTING UCSF Chimera 1.13 MODEL REFINEMENT PHENIX 1.16 MODEL REFINEMENT REFMAC 5
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION CTF amplitude correction was performed following 3D reconstruction. 233762 Images were binned and lowpass filtered for autopicking.