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Cryo-EM structure of "CT-CT dimer" of Lactococcus lactis pyruvate carboxylase with acetyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VYW
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.975 f_angle_d 0.626 f_chiral_restr 0.045 f_bond_d 0.005 f_plane_restr 0.003
Sample Pyruvate carboxylase with acetyl coenzyme A
Specimen Preparation Sample Aggregation State 3D ARRAY Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 1369092 Reported Resolution (Å) 2.15 Resolution Method FSC 0.143 CUT-OFF Other Details The particles were quadrupled for symmetry expansion (D2). The actual number of particles were 4*342273 Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (5VYW) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 48
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 900 Maximum Defocus (nm) 2400 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 81000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 3.0.6 IMAGE ACQUISITION EPU 2.4.0.54 CTF CORRECTION CTFFIND 4.1.5 MODEL FITTING PHENIX 1.18.2 MODEL REFINEMENT PHENIX 1.18.2 INITIAL EULER ASSIGNMENT RELION 3.06 FINAL EULER ASSIGNMENT RELION 3.1.0 RECONSTRUCTION RELION 3.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 4578464