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 1YXN | pdb_00001yxn

Pseudo-atomic model of a fiberless isometric variant of bacteriophage phi29


ELECTRON MICROSCOPY
Sample
Fiberless isometric phi29 capsid
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification Detailsfrozen in liquid ethane
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles5922
Reported Resolution (Å)7.9
Resolution Method
Other DetailsSoftware used included P3DR (3D reconstructions), PFT (initial orientation improvement), and POR (final orientation refinement.
Refinement Type
Symmetry TypePOINT
Point SymmetryI
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Targetrigid body refinement in real space against laplacian filtered EM density, using the program COLORES in the package SITUS. Each molecule in the T=3 asymmetric unit was refined separately.
Overall B Value
Fitting Procedure
DetailsMETHOD--6D search for each symmetry related molecule in the icosahedral asymmetric unit REFINEMENT PROTOCOL--rigid body
Data Acquisition
Detector TypeKODAK SO-163 FILM
Electron Dose (electrons/Å**2)20
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)100
Microscope ModelFEI/PHILIPS CM200FEG/ST
Minimum Defocus (nm)700
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification38000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGEMfit
MODEL FITTINGSITUS COLORES
MODEL FITTINGSITUS COLORES
RECONSTRUCTIONEM3DR
RECONSTRUCTIONPFT
RECONSTRUCTIONPOR
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
Inverse of CTF was applied to images. Both phases and amplitudes were corrected.