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Cryo-EM structure of Dengue virus serotype 3 in complex with human antibody 5J7 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3J6T experimental model PDB 3MA9 experimental model PDB 1DEE
Sample Dengue virus 3 complexed with human antibody 5J7 Fab Sample Components Dengue virus 3 Fab 5J7
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Blotted with filter paper for 2 seconds prior to snap freezing in liquid ethane (FEI VITROBOT MARK IV)
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 970 Reported Resolution (Å) 9 Resolution Method FSC 0.5 CUT-OFF Other Details (Single particle details: Particles were manually selected.) (Single particle--Applied symmetry: I) Refinement Type Symmetry Type POINT Point Symmetry I
Map-Model Fitting and Refinement Id 1 (3J6T, 3J6T, 3J6T, 3J6T, 3J6T, 3J6T, 3MA9, 1DEE) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target real space correlation Overall B Value Fitting Procedure Details REFINEMENT PROTOCOL--flexible DETAILS--Initially fitted in Chimera, model
rebuilt in Coot, refined in NAMD/MDFF
Data Acquisition Detector Type FEI FALCON I (4k x 4k) Electron Dose (electrons/Å**2) 18
Imaging Experiment 1 Date of Experiment 2012-03-23 Temperature (Kelvin) 100 Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 400 Maximum Defocus (nm) 4200 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 59000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version MODEL FITTING Coot MODEL FITTING MDFF MODEL FITTING NAMD MODEL FITTING UCSF Chimera RECONSTRUCTION EMAN 1 RECONSTRUCTION EMAN 2 RECONSTRUCTION MPSA
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details each particle