4V4U

The quasi-atomic model of Human Adenovirus type 5 capsid

ELECTRON MICROSCOPY

Sample
HUMAN ADENOVIRUS TYPE 5

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	ZEISS PLUNGE FREEZER CRYOBOX
Cryogen Name	ETHANE
Sample Vitrification Details	LIQUID ETHANE

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	4100
Reported Resolution (Å)	10
Resolution Method
Other Details	THE NUMBER OF ATOMS IN THIS STRUCTURE EXCEEDS THE MAXIMUM ALLOWED BY THE PDB FORMAT. IT HAS THEREFORE BEEN SPLIT ACROSS TWO PDB ENTRIES: 2BLD CONTAINS ...	THE NUMBER OF ATOMS IN THIS STRUCTURE EXCEEDS THE MAXIMUM ALLOWED BY THE PDB FORMAT. IT HAS THEREFORE BEEN SPLIT ACROSS TWO PDB ENTRIES: 2BLD CONTAINS THE PENTON BASE, 2BVI CONTAINS THE FOUR UNIQUE COPIES OF THE HEXON. THE COMPLETE CAPSID CAN BE GENERATED BY APPLYING ICOSAHEDRAL SYMMETRY OPERATORS TO THE COORDINATES IN THE TWO ENTRIES AND THEN COMBINING THE RESULTING CAPSID FRAGMENTS. THE PENTON BASE COMPRISES CHAINS A,B,C,D,E,S,T,U,V AND W AND MUST BE TRANSFORMED BY 12 SPECIFIC MATRICES DEFINED IN REMARK 350. THE HEXONS COMPRISE CHAINS F,G,H,I,J,K,L M,N,O,P AND Q AND MUST BE TRANSFORMED BY ALL ICOSAHEDRAL OPERATORS.
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1
Refinement Space	RECIPROCAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	R-FACTOR, CORRELATION COEFFICIENT
Overall B Value
Fitting Procedure
Details	METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY

Data Acquisition
Detector Type	KODAK SO-163 FILM
Electron Dose (electrons/Å**2)	10

Imaging Experiment	1
Date of Experiment	2003-10-01
Temperature (Kelvin)	95
Microscope Model	FEI/PHILIPS CM200T
Minimum Defocus (nm)	100
Maximum Defocus (nm)	250
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	27500
Calibrated Magnification	28600
Source	LAB6
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
CTF CORRECTION	CTFMIX
MODEL FITTING	Situs
MODEL FITTING	URO
PARTICLE SELECTION	X3D
RECONSTRUCTION	EM3DR
RECONSTRUCTION	PFT	2
RECONSTRUCTION	SPIDER

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	AMPLITUDE, PHASE TMV AND COMPARISON WITH X-RAY DATA

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.