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Murine core lysosomal multienzyme complex (LMC) composed of acid beta-galactosidase (GLB1) and protective protein cathepsin A (PPCA, CTSA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3THC experimental model PDB 1IVY
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.3462 f_angle_d 0.8386 f_chiral_restr 0.048 f_plane_restr 0.0066 f_bond_d 0.0042
Sample core lysosomal multienzyme complex composed of CTSA and GLB1
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 17591 Reported Resolution (Å) 4.59 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry D3
Map-Model Fitting and Refinement Id 1 (3THC, 1IVY) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value 116 Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 41
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 75000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details two datasets: untilted and 40 degrees tilted
EM Software Task Software Package Version CTF CORRECTION cryoSPARC 2 MODEL FITTING UCSF Chimera MODEL REFINEMENT PHENIX INITIAL EULER ASSIGNMENT cryoSPARC 2 FINAL EULER ASSIGNMENT cryoSPARC 2 CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION Patch CTF implemented in cryoSPARC V2