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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 experimental model PDB 1NL0 in silico model AlphaFold AF-F2RM35-F1-v4 experimental model PDB 9ZQY
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.937 f_angle_d 0.756 f_chiral_restr 0.053 f_plane_restr 0.005 f_bond_d 0.004
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
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 78076 Reported Resolution (Å) 3.65 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 78076 Reported Resolution (Å) 3.65 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 78076 Reported Resolution (Å) 3.65 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 78076 Reported Resolution (Å) 3.65 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1 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 Rigid fit, backbone trace, and ab-initio
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) FEI FALCON IV (4k x 4k) FEI FALCON IV (4k x 4k) FEI FALCON IV (4k x 4k) FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 60 57.2 52.5 52.5 50
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 4.7.1 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.7.1 MODEL FITTING UCSF ChimeraX 1.10 MODEL REFINEMENT PHENIX 1.21.2_5419 MODEL REFINEMENT Coot 0.9.8.95 CLASSIFICATION cryoSPARC 4.7.1 RECONSTRUCTION cryoSPARC 4.7.1 PARTICLE SELECTION cryoSPARC 4.7.1 CTF CORRECTION cryoSPARC 4.7.1 CLASSIFICATION cryoSPARC 4.7.1 RECONSTRUCTION cryoSPARC 4.7.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 682170 PHASE FLIPPING AND AMPLITUDE CORRECTION 682170