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Cryo-EM structure of yeast Elp123 in complex with alanine tRNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QK7 experimental model PDB 1EHZ
Sample Yeast Elp123 in complex with alanine tRNA
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 15 s wait time, blot force 5, 5 s blot time
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 16809 Reported Resolution (Å) 3.96 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6QK7, 1EHZ) Refinement Space Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details After initial rigid body fit, further fitting was done using MDFF and NAMDINATOR
Data Acquisition Detector Type GATAN K2 QUANTUM (4k x 4k) Electron Dose (electrons/Å**2) 42.45
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 800 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 165000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC v3.2.0 IMAGE ACQUISITION SerialEM CTF CORRECTION RELION 3.1 MODEL FITTING UCSF ChimeraX MODEL REFINEMENT PHENIX INITIAL EULER ASSIGNMENT cryoSPARC v3.2.0 FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 172149 given number of particles is after TOPAZ picking and Ab-Initio classification