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Structure of a complex between Pasteurella multocida surface lipoprotein, PmSLP-1, and bovine complement factor I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.314 f_angle_d 0.707 f_chiral_restr 0.046 f_plane_restr 0.005 f_bond_d 0.003
Sample Dimeric complex of PmSLP-1 and complement factor I
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 3.5ul of sample was applied to the grid, followed by 5 s blotting
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 200426 Reported Resolution (Å) 4 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 REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details Initial local fitting was done using ChimeraX. Iterative rounds of model building and real-space refinement was done using Coot and PHENIX
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 1200 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 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.2.1 IMAGE ACQUISITION SerialEM MODEL FITTING UCSF ChimeraX 1.6.1 MODEL REFINEMENT 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 1938372 Blob picker was used for initial particle selection