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CryoEM structure of the Ectodomain of Human PLA2R
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JPT
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.5873 f_angle_d 0.628 f_chiral_restr 0.0428 f_plane_restr 0.0045 f_bond_d 0.0031
Sample Human PLA2R Ectodomain
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 221000 Reported Resolution (Å) 3.4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7JPT) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Correlation Coefficient Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 14.8 14.2
Imaging Experiment 1 2 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS FEI TITAN KRIOS Minimum Defocus (nm) 800 800 Maximum Defocus (nm) 2000 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN FIELD EMISSION GUN Acceleration Voltage (kV) 300 300 Imaging Details 30 degree Tilt dataset
EM Software Task Software Package Version MODEL FITTING PHENIX 1.19.2 MODEL REFINEMENT PHENIX 1.19.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1700000 Particles were picked using a Gaussian blob (80-130 ang) from 100 images of the 0 deg data set were extracted in a 256 pixel box, binned 4x4 (64 pixel box), and subjected to 2D classification. The best templates were used to template pick all images from both data sets.