3J6R | pdb_00003j6r

Electron cryo-microscopy of Human Papillomavirus Type 16 capsid

ELECTRON MICROSCOPY

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Starting Model(s)

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

Sample
Human Papilloma Virus type 16 capsid

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA KF80
Cryogen Name	ETHANE
Sample Vitrification Details	Plunged into liquid ethane (LEICA KF80)

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	5952
Reported Resolution (Å)	9.1
Resolution Method	FSC 0.33 CUT-OFF
Other Details	(Single particle--Applied symmetry: I)
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (1DZL)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--flexible DETAILS--Rigid fitting of domain copies in asymmetric unit, followed by molecular dynamics-based flexible fitting, adding symmetry as constraint

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

Imaging Experiment	1
Date of Experiment	2010-02-02
Temperature (Kelvin)
Microscope Model	FEI/PHILIPS CM200FEG
Minimum Defocus (nm)	537
Maximum Defocus (nm)	2175
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	GATAN LIQUID NITROGEN
Nominal Magnification	38000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	120
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	MDFF
MODEL FITTING	NAMD
MODEL FITTING	PyMOL
MODEL FITTING	UCSF Chimera
MODEL FITTING	VMD
RECONSTRUCTION	Auto3DEM
RECONSTRUCTION	Bsoft

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	each micrograph