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Cryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Propionyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation s_dihedral_angle_6_deg 15.5369 s_dihedral_angle_3_deg 10.709 s_dihedral_angle_1_deg 7.4255 s_dihedral_angle_2_deg 6.0168 s_angle_nonh_deg 1.9935 s_nbtor 0.2149 s_nbd 0.2051 s_hbond_nbd 0.0918 s_chiral_restr 0.0794 s_bond_nonh_d 0.0102
RMS Deviations Key Refinement Restraint Deviation s_dihedral_angle_6_deg 15.5369 s_dihedral_angle_3_deg 10.709 s_dihedral_angle_1_deg 7.4255 s_dihedral_angle_2_deg 6.0168 s_angle_nonh_deg 1.9935 s_nbtor 0.2149 s_nbd 0.2051 s_hbond_nbd 0.0918 s_chiral_restr 0.0794 s_bond_nonh_d 0.0102 s_planes 0.0069
Sample Cryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Propionyl-CoA
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE-PROPANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 52469 Reported Resolution (Å) 2.4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 44.4
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 2250 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 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.4.1 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.4.1 MODEL FITTING UCSF ChimeraX 1.10.1 MODEL REFINEMENT Servalcat INITIAL EULER ASSIGNMENT cryoSPARC 4.4.1 FINAL EULER ASSIGNMENT cryoSPARC 4.4.1 CLASSIFICATION cryoSPARC 4.4.1 RECONSTRUCTION cryoSPARC 4.4.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 6398521