1M4X

PBCV-1 virus capsid, quasi-atomic model


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J5Q 
experimental modelPDB 1M3Y 
Sample
PBCV-1 virus capsid
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification Instrument
Cryogen Name
Sample Vitrification Detailsfrozen in liquid propane
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles
Reported Resolution (Å)28
Resolution Method
Other Detailsused Tim Baker's programs PFT, EM3DR, etc.
Refinement Type
Symmetry TypePOINT
Point SymmetryI
Map-Model Fitting and Refinement
Id1 (1J5Q, 1M3Y)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Targetrigid 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
DetailsMETHOD--6d search, separately for each symmetry related molecule in the icosahedral ASU. REFINEMENT PROTOCOL--rigid body
Data Acquisition
Detector TypeKODAK SO-163 FILM
Electron Dose (electrons/Å**2)
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)100
Microscope ModelFEI/PHILIPS CM200FEG/ST
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGSitus
RECONSTRUCTIONOTHER
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
inverse of CTF was applied to images