3J7G

Electron cryo-microscopy of human papillomavirus 16 and H16.V5 Fab fragments

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OAE

Sample
Mature HPV16 quasivirus capsid complexed with H16.V5 Fabs
Sample Components
Human papillomavirus 16
H16.V5 Fab

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	GATAN CRYOPLUNGE 3
Cryogen Name	ETHANE
Sample Vitrification Details	Blot for 0.7 seconds before plunging into liquid ethane (GATAN CRYOPLUNGE 3).

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	2075
Reported Resolution (Å)	13.6
Resolution Method	FSC 0.5 CUT-OFF
Other Details	Semi-automatic particle selection was performed using e2boxer.py to obtain the particle coordinates, followed by particle boxing, linearization, norma ...	Semi-automatic particle selection was performed using e2boxer.py to obtain the particle coordinates, followed by particle boxing, linearization, normalization, and apodization of the images using Robem. Defocus and astigmatism values to perform contrast transfer function (CTF) correction were assessed using Robem for the extracted particles. The icosahedrally averaged reconstructions were initiated using a random model generated with setup_rmc and reached 14 A resolution estimated at a Fourier Shell Correlation (FSC) of 0.5. For the last step of refinement, the final maps were CTF-corrected using a B factor of 200 A2. (Single particle--Applied symmetry: I)
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (3OAE)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--flexible

Data Acquisition
Detector Type	GATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å**2)	15

Imaging Experiment	1
Date of Experiment	2013-10-30
Temperature (Kelvin)	95
Microscope Model	JEOL 2100
Minimum Defocus (nm)	690
Maximum Defocus (nm)	3990
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	GATAN LIQUID NITROGEN
Nominal Magnification	80000
Calibrated Magnification
Source	LAB6
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	Situs
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	Auto3DEM
RECONSTRUCTION	EMAN	2

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	Each particle

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 R01GM157729.