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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