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Structural insights into the exosite-mediated activation of Factor IX by Factor XIa using cryoEM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6I58 in silico model AlphaFold AF-F2RM35-F1-v4 experimental model PDB 1NL0 experimental model PDB 9ZQY
Sample Complex of Factor XIa (FXIa) with Factor IX (FIX). Sample Components Activated coagulation Factor XI (FXIa) Coagulation Factor IX (FIX)
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Quantifoil R1.2/1.3 Gold ultrafoil - 300 mesh - glow discharged for 20 seconds using atmospheric air
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 87309 Reported Resolution (Å) 3.4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 87309 Reported Resolution (Å) 3.4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6I58, 1NL0, 9ZQY) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details Combined Ab-initio for FXIa and Rigid fit and backbone trace for FIX
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 56 57.2
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS GLACIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2400 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 150000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 5.0.2 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 5.0.2 MODEL FITTING UCSF ChimeraX 1.10 CLASSIFICATION cryoSPARC 5.0.2 RECONSTRUCTION cryoSPARC 5.0.2 PARTICLE SELECTION cryoSPARC 5.0.2 CTF CORRECTION cryoSPARC 5.0.2 CLASSIFICATION cryoSPARC 4.7.1 RECONSTRUCTION cryoSPARC 5.0.2 MODEL REFINEMENT PHENIX 1.21.2_5419 MODEL REFINEMENT Coot 0.9.8.95
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1544517 PHASE FLIPPING AND AMPLITUDE CORRECTION 1544517