ELECTRON MICROSCOPY

Sample

Assembled scaffold-like particle of A17(1-16) peptide-bound Vaccinia virus D13

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument ?
Cryogen Name ETHANE
Sample Vitrification Details Wait time: 10sec Blot force: 0 Blot time: 5sec
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 643673
Reported Resolution (Å) 3.63
Resolution Method FSC 0.143 CUT-OFF
Other Details ?
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol RIGID BODY FIT
Refinement Target Map-to-model correlation
Overall B Value 161
Fitting Procedure ?
Details Model building was proceeded by manually fitting the cryo-EM structure of D13 (PDB ID 7VFD) into our cryo-EM map using UCSF Chimera. The model was subsequently inspected and adjusted in Coot. Coordinate refinements were performed using the real-space refinement routine in the Phenix software suite.
Data Acquisition
Detector Type GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å2) 45.5
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model TFS KRIOS
Minimum Defocus (nm) 1500
Maximum Defocus (nm) 2500
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS ?
Imaging Mode BRIGHT FIELD
Specimen Holder Model ?
Nominal Magnification 42000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC 4.7.1
IMAGE ACQUISITION EPU 3
CTF CORRECTION cryoSPARC 4.7.1
MODEL FITTING UCSF Chimera ?
MODEL FITTING Coot 0.9.8.92
INITIAL EULER ASSIGNMENT cryoSPARC 4.7.1
FINAL EULER ASSIGNMENT cryoSPARC 4.7.1
CLASSIFICATION cryoSPARC 4.5.3
RECONSTRUCTION cryoSPARC 4.7.1
MODEL REFINEMENT PHENIX 1.21.2_5419
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
NONE ?
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