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Cryo-EM structure of the dihydrolipoyl transacetylase cubic core of the E. coli pyruvate dehydrogenase complex including lipoyl domains
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N72 experimental model PDB 1QJO
Sample dihydrolipoyl transacetylase cubic core of the pyruvate dehydrogenase complex
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 3 microliters of sample, blot force 0, 15 second wait time, 3 second blot time Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 3 microliters of sample, blot force 0, 15 second wait time, 3 second blot time Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 2.5 microliters of sample, blot force 0, 15 second wait time, 3 second blot time
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 29434 Reported Resolution (Å) 3.16 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry O
Map-Model Fitting and Refinement Id 1 (4N72, 1QJO) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 QUANTUM (4k x 4k) GATAN K2 QUANTUM (4k x 4k) GATAN K2 QUANTUM (4k x 4k) Electron Dose (electrons/Å**2) 30 28.11 28.11
Imaging Experiment 1 2 3 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS FEI TITAN KRIOS FEI TITAN KRIOS Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 2.7 2.7 Imaging Mode BRIGHT FIELD BRIGHT FIELD BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN FIELD EMISSION GUN FIELD EMISSION GUN Acceleration Voltage (kV) 300 300 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 2.15 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 2.15 MODEL FITTING PHENIX 1.16 INITIAL EULER ASSIGNMENT cryoSPARC 2.15 FINAL EULER ASSIGNMENT cryoSPARC 2.15 CLASSIFICATION cryoSPARC 2.15 RECONSTRUCTION cryoSPARC 2.15 MODEL REFINEMENT PHENIX 1.16 MODEL REFINEMENT REFMAC 5.8.0232
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 799790 automated template picking in CryoSPARC