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Cryo EM structure of alpha-glucosidase (yicI) from Klebsiella aerogenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8T7Z
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.772 f_angle_d 0.415 f_chiral_restr 0.042 f_plane_restr 0.003 f_bond_d 0.002
Specimen Preparation Sample Aggregation State 2D ARRAY Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 153600 Reported Resolution (Å) 3.19 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type 3D CRYSTAL Point Symmetry D3
Map-Model Fitting and Refinement Id 1 (8T7Z) 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) 60.39
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 200 Maximum Defocus (nm) 600 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode 4D-STEM Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 81000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Appion IMAGE ACQUISITION Leginon MASKING cryoSPARC CTF CORRECTION cryoSPARC LAYERLINE INDEXING cryoSPARC DIFFRACTION INDEXING cryoSPARC MODEL FITTING UCSF ChimeraX MODEL REFINEMENT PHENIX 2.0_5778: INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 925341