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Cryo-EM structure of human Elp123 in complex with tRNA, acetyl-CoA, 5'-deoxyadenosine and methionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-O95163-F1 in silico model AlphaFold AF-Q6IA86-F1 in silico model AlphaFold AF-Q9H9T3-F1
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.846 f_angle_d 0.564 f_chiral_restr 0.043 f_plane_restr 0.004 f_bond_d 0.003
Sample Human Elp123 in complex with glutamine tRNA, acetyl-CoA, 5'-deoxyadenosine and methionine
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 215353 Reported Resolution (Å) 2.87 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 40.09
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 900 Maximum Defocus (nm) 2100 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version 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 1250013 given number of particles is the sum of blob and 3x TOPAZ pickings, each firstly curated in 2D classification