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Cryo- EM structure of ribosomal large subunit (LSU) from Entamoeba histolytica at 2.8 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XXB experimental model PDB 4UG0
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.4775 f_angle_d 0.5729 f_chiral_restr 0.0387 f_plane_restr 0.0041 f_bond_d 0.0036
Sample Entamoeba histolytica Ribosome Large Subunit
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 378061 Reported Resolution (Å) 2.8 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (5XXB, 4UG0) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value 67.76 Fitting Procedure Details phenix.real_space_refinement
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 1.34
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1800 Maximum Defocus (nm) 3000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification Calibrated Magnification 75000 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version MODEL REFINEMENT PHENIX dev_svn
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 763731