3J8V | pdb_00003j8v

Cryo-EM reconstruction of quasi-HPV16 complex with H16.14J Fab

ELECTRON MICROSCOPY

Starting Model(s)

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

Sample
Quasi-human papillomavirus 16 complexed with H16.14J Fab
Sample Components
Human papillomavirus 16
H16.14J 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	5642
Reported Resolution (Å)	13.9
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 necessary to perform contrast transfer function (CTF) correction for the extracted particles were assessed using Robem. The icosahedrally averaged reconstruction was initiated using a random model generated with setup_rmc. 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, 3OAE, 3OAE, 3OAE, 3OAE)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--rigid body

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

Imaging Experiment	1
Date of Experiment	2014-08-27
Temperature (Kelvin)	95
Microscope Model	JEOL 2100
Minimum Defocus (nm)	620
Maximum Defocus (nm)	4690
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	GATAN LIQUID NITROGEN
Nominal Magnification	50000
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.