6ODM

Herpes simplex virus type 1 (HSV-1) portal vertex-adjacent capsid/CATC, asymmetric unit

ELECTRON MICROSCOPY

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	4.6096
f_angle_d	0.9211
f_chiral_restr	0.052
f_plane_restr	0.007
f_bond_d	0.0048

Sample
Human herpesvirus 1 strain KOS

Specimen Preparation
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
Point Symmetry	C5

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 Co ...	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/Å**2)	25

Imaging Experiment	1
Date of Experiment
Temperature (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

EM Software
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		45445

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.