1M4X | pdb_00001m4x

PBCV-1 virus capsid, quasi-atomic model

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1J5Q
experimental model	PDB	1M3Y

Sample
PBCV-1 virus capsid

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument
Cryogen Name
Sample Vitrification Details	frozen in liquid propane

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles
Reported Resolution (Å)	28
Resolution Method
Other Details	used Tim Baker's programs PFT, EM3DR, etc.
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (1J5Q, 1M3Y)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	rigid body refinement in real space against Lagrangian filtered EM density, using the program SITUS.Each molecule in the icosahedral ASU was refined separately.
Overall B Value
Fitting Procedure
Details	METHOD--6d search, separately for each symmetry related molecule in the icosahedral ASU. REFINEMENT PROTOCOL--rigid body

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

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)	100
Microscope Model	FEI/PHILIPS CM200FEG/ST
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	Situs
RECONSTRUCTION	OTHER

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	inverse of CTF was applied to images