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Cryo-EM structure of Lactococcus lactis pyruvate carboxylase with acetyl-CoA and cyclic di-AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VYZ
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.417 f_angle_d 0.675 f_chiral_restr 0.044 f_plane_restr 0.005 f_bond_d 0.004
Sample Pyruvate carboxylase with acetyl coenzyme A and cyclic di-AMP
Specimen Preparation Sample Aggregation State 3D ARRAY Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 2090256 Reported Resolution (Å) 3.29 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (5VYZ) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 95
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 2200 Maximum Defocus (nm) 3700 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 75000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Xmipp IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND 4.1 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 3.1.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2172689