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Title:Cryo-electron microscopic reconstruction of wild rabbit hemorrhagic disease virus
Authors:Wang X, Xu F, Liu J, Gao B, Zhang K, Zhai Y, Ma J, Hu Z, Pang X, Zheng D, Pang H, Sun F
Sample:Wild Rabbit Hemorrhagic Disease Virus (strain HYD)
Method:Single particle reconstruction (6.5 angstroms resolution)
Red flagLatest update:2013-02-06
Sample
Sample name: Wild Rabbit Hemorrhagic Disease Virus (strain HYD)
Theoretical molecular weight of the sample: 10.8
Components:
ID Type Name Exp. MW (MDa) Oligomeric details Recombinant expression Synthetic Organism UniProt identifier GO identifier InterPro identifier Virus identifier Details
1virusRabbit hemorrhagic disease virusRabbit hemorrhagic disease virusHYD strain and gene bank number is AEB26305.
Experiment
Specimen state: Particle
Specimen preparation:
pHSpecimen conc.DetailsStainingSpecimen support details
7.0 mg/mL50mM Tris, 50mM NaCl, 5mM EDTA200 mesh copper grid with holey array carbon support (GiG), glow discharged
Vitrification:
Cryogen nameHumidityTemp.Instr.MethodTime resolvedDetails
ETHANE100%100 KFEI VITROBOT MARK IVBlot for 3 seconds before plunging ms
Imaging:
MicroscopeVoltageIllumination modeImaging modeCsDefocus min.Defocus max.Nominal mag.Calibrated mag.Electron sourceDetectorDetector distanceAstigmatism
FEI TITAN KRIOS300 kVFLOOD BEAMBRIGHT FIELD2.7 mm1500 nm2500 nm96000160770FIELD EMISSION GUNGATAN ULTRASCAN 4000 (4k x 4k) mmObjective lens astigmatism was corrected at 100,000 times magnification

Specimen holderHolder modelTilt min.Tilt max.Energy filterEnergy windowTemp.Temp. min.Temp. max.Beam tiltElectron doseOther detailsDate
Liquid nitrogen cooledFEI TITAN KRIOS AUTOGRID HOLDER eV85 K K K0 mrad20 e/Å222-JAN-2011
Processing
Protocol:Projection matching and Fourier reconstruction
Software:EMAN1.9, Spider
CTF correction:CTF correction of each whole micrograph
Number of particles:26000
Number of class averages:475
Imposed symmetry:I
Resolution by author:6.5 Å
Resolution method:FSC 0.5
Processing details:The final map was sharpened to 4.5 Angstrom with B factor -300 and then filtered to 5.0 Angstrom. The particles were selected using an automatic selection program FindEM.
Scanned images:
Num. imagesSampling sizeOD rangeQuant. bit numberOther detailsScanner
110015 μm/pixel32
Fitting:
PDBProtocolTarget crit.SoftwareB valueFitting spacePDB chainDetails
4EGT rigid bodyChimeraREALProtocol: Rigid body. The P domains were separately fitted into the map by automatic rigid body fitting using Chimera (FIT IN MAP).
4EJR rigid bodyChimeraREALProtocol: Rigid body. The S domains were separately fitted into the map by automatic rigid body fitting using Chimera (FIT IN MAP).