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A model of the EIAV CA-SP hexamer (C2) from Gag-deltaMA tubes assembled at pH6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EIA
Sample Equine infectious anemia virus
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK II Cryogen Name ETHANE Sample Vitrification Details 1-2 seconds blot time, offset -3mm
3D Reconstruction Reconstruction Method SUBTOMOGRAM AVERAGING Number of Particles 112929 Reported Resolution (Å) 3.8 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 (2EIA) Refinement Space REAL Refinement Protocol OTHER Refinement Target Cross-correlation coefficient Overall B Value Fitting Procedure Details Rigid body fitting was done in Chimera. Missing residues were built de novo in Coot.
Refinement was performed iteratively in Phenix and Coot.
Data Acquisition Detector Type GATAN K2 QUANTUM (4k x 4k) Electron Dose (electrons/Å**2) 3.4
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) -1500 Maximum Defocus (nm) -3500 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 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details nanoprobe
EM Software Task Software Package Version VOLUME SELECTION MATLAB IMAGE ACQUISITION SerialEM CTF CORRECTION CTFFIND 4 CTF CORRECTION NOVACTF MODEL FITTING UCSF Chimera MODEL FITTING Coot FINAL EULER ASSIGNMENT AV3 FINAL EULER ASSIGNMENT TOM Toolbox RECONSTRUCTION AV3 RECONSTRUCTION TOM Toolbox MODEL REFINEMENT PHENIX MODEL REFINEMENT Coot
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION CTF-correction was performed using NOVACTF