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Cryo-EM structure of Heyndrickxia coagulans beta-galactosidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TTY
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.3727 f_angle_d 0.9561 f_chiral_restr 0.0578 f_plane_restr 0.0166 f_bond_d 0.0055
Sample beta-galactosidase hexamer
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 629632 Reported Resolution (Å) 2.97 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry D3
Map-Model Fitting and Refinement Id 1 (3TTY) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 45
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS GLACIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 2000 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) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.6.0 CTF CORRECTION cryoSPARC 4.6.0 MODEL FITTING UCSF ChimeraX 1.10.1 MODEL REFINEMENT PHENIX 1.21.2_5419 INITIAL EULER ASSIGNMENT cryoSPARC 4.6.0 FINAL EULER ASSIGNMENT cryoSPARC 4.6.0 RECONSTRUCTION cryoSPARC 4.6.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 799865