6ODM

ELECTRON MICROSCOPY

Sample

Human herpesvirus 1 strain KOS

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument HOMEMADE PLUNGER
Cryogen Name ETHANE
Sample Vitrification Details The sample was manually blotted and frozen with a homemade plunger.
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 42857
Reported Resolution (Å) 4.3
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 FLEXIBLE FIT
Refinement Target ?
Overall B Value 100
Fitting Procedure ?
Details Capsid and CATC atomic models from Dai & Zhou, Science 2018 (PDB-6CGR) were docked into the C5 portal vertex map (EMD-9860) and manually refined in Coot to improve fit. Regions demonstrating major differences were reconstructed ab initio. Models were then iteratively refined between real space refinement in PHENIX and manual refinement in Coot.
Data Acquisition
Detector Type GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å2) 25
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) ?
Maximum Defocus (nm) ?
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 14000
Calibrated Magnification 24271
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION EMAN 1.09
IMAGE ACQUISITION Leginon ?
CTF CORRECTION CTFFIND 3.0
CTF CORRECTION RELION 2.1
MODEL FITTING Coot 0.8.6.1
INITIAL EULER ASSIGNMENT RELION 2.1
FINAL EULER ASSIGNMENT RELION 2.1
RECONSTRUCTION RELION 2.1
MODEL REFINEMENT PHENIX 1.13
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?