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Cryo-EM structure of the C terminal region of PTX3 with a section of coiled-coil
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8PVQ
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.683 f_angle_d 0.5 f_chiral_restr 0.045 f_bond_d 0.003 f_plane_restr 0.003
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 23457 Reported Resolution (Å) 3.33 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry D4
Map-Model Fitting and Refinement Id 1 (8PVQ) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target RSC Overall B Value Fitting Procedure Details Initial fitting was done using chimera followed by real-space refinement in phenix and rebuilding in COOT
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 165000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.3.1 MODEL FITTING UCSF Chimera 1.13.1 INITIAL EULER ASSIGNMENT cryoSPARC 4.3.1 FINAL EULER ASSIGNMENT cryoSPARC 4.3.1 MODEL REFINEMENT PHENIX 1.19
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE