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Cryo-EM structure of the GPI inositol-deacylase (PGAP1/Bst1) from Chaetomium thermophilum
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.344 f_angle_d 0.575 f_chiral_restr 0.041 f_plane_restr 0.005 f_bond_d 0.002
Sample GPI inositol-deacylase
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Blot for 4.5s before plunging
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 407921 Reported Resolution (Å) 2.84 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 Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1200 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC v3.3.2 CTF CORRECTION CTFFIND ctffind4 MODEL REFINEMENT PHENIX INITIAL EULER ASSIGNMENT cryoSPARC v3.3.2 FINAL EULER ASSIGNMENT cryoSPARC v3.3.2 CLASSIFICATION cryoSPARC v3.3.2 RECONSTRUCTION cryoSPARC v3.3.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION