3J1P

Atomic model of rabbit hemorrhagic disease virus


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4EGT 
experimental modelPDB 4EJR 
Sample
Wild Rabbit Hemorrhagic Disease Virus (strain HYD)
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsBlot for 3 seconds before plunging into liquid ethane.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles26000
Reported Resolution (Å)6.5
Resolution MethodFSC 0.5 CUT-OFF
Other DetailsThe final map was sharpened to 4.5 Angstrom with B factor -300 and then filtered to 5.0 Angstrom (details about the particle: the particles were selec ...The final map was sharpened to 4.5 Angstrom with B factor -300 and then filtered to 5.0 Angstrom (details about the particle: the particles were selected using an automatic selection program FindEM).
Refinement Type
Symmetry TypePOINT
Point SymmetryI
Map-Model Fitting and Refinement
Id1 (4EGT)2 (4EJR)3
Refinement SpaceREALREALREAL
Refinement ProtocolFLEXIBLE FITFLEXIBLE FITOTHER
Refinement Target
Overall B Value
Fitting Procedure
DetailsREFINEMENT PROTOCOL--symmetry restrained molecular dynamics flexible fitting DETAILS--The P domains were separately fitted into the map by automatic ...REFINEMENT PROTOCOL--symmetry restrained molecular dynamics flexible fitting DETAILS--The P domains were separately fitted into the map by automatic rigid body fitting using Chimera (FIT IN MAP).
REFINEMENT PROTOCOL--symmetry restrained molecular dynamics flexible fitting DETAILS--The S domains were separately fitted into the map by automatic ...REFINEMENT PROTOCOL--symmetry restrained molecular dynamics flexible fitting DETAILS--The S domains were separately fitted into the map by automatic rigid body fitting using Chimera (FIT IN MAP).
REFINEMENT PROTOCOL--Manual building of NTA domain DETAILS--The N-terminal NTA domain was manually built according to the high resolution EM map.
Data Acquisition
Detector TypeGATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å**2)20
Imaging Experiment1
Date of Experiment2011-01-22
Temperature (Kelvin)85
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1500
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelOTHER
Nominal Magnification96000
Calibrated Magnification160770
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGCoot
MODEL FITTINGUCSF Chimera
RECONSTRUCTIONEMAN1.9
RECONSTRUCTIONSPIDER
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
CTF correction of each whole micrograph