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Structure of the mammalian 60S ribosomal subunit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3J3B experimental model PDB 3J3F
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.912 r_dihedral_angle_1_deg 28.519 r_dihedral_angle_4_deg 23.161 r_dihedral_angle_3_deg 22.703 r_mcangle_it 3.214 r_angle_refined_deg 1.916 r_mcbond_it 1.814 r_mcbond_other 1.813 r_angle_other_deg 1.621 r_chiral_restr 0.615
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.912 r_dihedral_angle_1_deg 28.519 r_dihedral_angle_4_deg 23.161 r_dihedral_angle_3_deg 22.703 r_mcangle_it 3.214 r_angle_refined_deg 1.916 r_mcbond_it 1.814 r_mcbond_other 1.813 r_angle_other_deg 1.621 r_chiral_restr 0.615 r_gen_planes_refined 0.02 r_bond_refined_d 0.011 r_bond_other_d 0.005 r_gen_planes_other 0.005
Sample The 60S ribosomal subunit purified from porcine pancreas
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 3 uL sample was incubated on the grid for 30 seconds and blotted for 9 seconds before being plunged into liquid ethane (FEI VITROBOT MARK IV).
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 80019 Reported Resolution (Å) 3.4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (3J3B, 3J3F) Refinement Space RECIPROCAL Refinement Protocol OTHER Refinement Target R-factor and FSC Overall B Value 37 Fitting Procedure Details METHOD--Maximum likelihood
Data Acquisition Detector Type FEI FALCON II (4k x 4k) Electron Dose (electrons/Å**2) 27
Imaging Experiment 1 Date of Experiment 2014-04-07 Temperature (Kelvin) 70 Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 2500 Maximum Defocus (nm) 3500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 59000 Calibrated Magnification 104478 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version MODEL FITTING REFMAC MODEL FITTING REFMAC RECONSTRUCTION RELION
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details Each particle