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Cryo-EM structure of factor Va bound to activated protein C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9MOT in silico model AlphaFold AF-P04070-F1-V4
Sample Complex of coagulation Factor Va and Activated Protein C Sample Components Coagulation Factor Va Activated Protein C
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 Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 384239 Reported Resolution (Å) 3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (9MOT, 1lqv) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
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) FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 51.86 46.6 46.89 47.19 46.89 52.8
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 0.01 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 75000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.6.2 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.6.2 MODEL FITTING UCSF ChimeraX 1.9 RECONSTRUCTION cryoSPARC 4.6.2 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