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Capsid structure of the L-A helper virus from native viral communities
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M1C
Sample Saccharomyces cerevisiae virus L-A
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details blot force 2 and blot time 6 s before plunging
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 1020420 Reported Resolution (Å) 3.78 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (1M1C) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details The initial model was rigid-fitted by ChimeraX and refined by iterative cycles of Coot and PHENIX.
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 30
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS GLACIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2000 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 92000 Calibrated Magnification 89297 Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC v3.3 IMAGE ACQUISITION EPU 2.11.1.11REL CTF CORRECTION cryoSPARC v.3.3 MODEL FITTING UCSF ChimeraX 1.3 MODEL REFINEMENT Coot 0.9.6 MODEL REFINEMENT PHENIX dev-4379 CLASSIFICATION cryoSPARC v3.3 RECONSTRUCTION cryoSPARC v3.3
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE 2725140