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Lysosomal transporting complex of beta-glucocerebrosidase (GCase) and lysosomal integral membrane protein 2 (LIMP-2) with bound Pro-macrobodies (Combined focus map)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TN1 experimental model PDB 4Q4F experimental model PDB 9ENA
Sample Lysosomal transporting complex of beta-glucocerebrosidase and lysosomal integral membrane protein 2 (LIMP-2) with two bound Pro-macrobodies.
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 397385 Reported Resolution (Å) 3.7 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6TN1) 2 (4Q4F) 3 (9ENA) Refinement Space REAL REAL REAL Refinement Protocol FLEXIBLE FIT FLEXIBLE FIT RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details Initial fitting with ChimeraX, manual flexible fitting with Coot, refinement with Phenix Initial fitting with ChimeraX, manual flexible fitting with Coot, refinement with Phenix Initial fitting with ChimeraX, manual flexible fitting with Coot, refinement with Phenix
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS GLACIOS Minimum Defocus (nm) 600 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.2 IMAGE ACQUISITION EPU MASKING UCSF ChimeraX 1.7.1 MASKING cryoSPARC 4.2 CTF CORRECTION cryoSPARC 4.2 MODEL FITTING Coot WinCoot 0.9.8.7 MODEL FITTING UCSF ChimeraX 1.7.1 MODEL REFINEMENT PHENIX OTHER MODELLER CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC MODEL REFINEMENT PHENIX 1.20.1_4487 MODEL FITTING Coot WinCoot 0.9.8.7 MODEL FITTING UCSF ChimeraX 1.7.1 MODEL REFINEMENT PHENIX 1.20.1_4487 MODEL FITTING Coot WinCoot 0.9.8.7 MODEL FITTING UCSF ChimeraX 1.7.1 MODEL REFINEMENT PHENIX 1.20.1_4487 RECONSTRUCTION PHENIX 1.20.1_4487
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION