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Title:Conservation of the capsid structure in tailed dsDNA bacteriophages: the pseudoatomic structure of phi29.
Authors:M.C. Morais, K.H. Choi, J.S. Koti, P.R. Chipman, Anderson, D.L., Rossmann, M.G. Chipman, D.L. Anderson, M.G. Rossmann
Sample:phi29 fiberless isometric particle
Aggregation state:Icosahedral (7.9 angstroms resolution)
Red flagLatest update:2011-05-26
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Sample
Sample name: phi29 fiberless isometric particle
Oligomeric state: particle forms an T3 icosahedron
Theoretical molecular weight of the sample: 8.97
Components:
ID Type Name Exp. MW (MDa) Oligomeric details Recombinant expression Synthetic Organism GO identifier InterPro identifier Virus identifier Details
1virusbacteriophage phi298.97bacteriophage phi29
Experiment
Sample preparation:
pHSample conc.DetailsStainingSample support details
7.8 mg/mL25 mM Tris-HCl 5 mM MgCl2 50 mM NaCl 5 mM sodium azide
Vitrification:
Cryogen nameHumidityTemp.Instr.MethodTime resolvedDetails
ETHANE% K ms
Imaging:
MicroscopeVoltageIllumination modeImaging modeCs:Defocus min.Defocus max.Nominal mag.Calibrated mag.Electron sourceDetectorDetector distanceAstigmatism
FEI/PHILIPS CM200FEG200 kVFLOOD BEAMBRIGHT FIELD2.0 mm700 nm3000 nm38000FIELD EMISSION GUNKodak SO163 film mm

Specimen holderHolder modelTilt min.Tilt max.Energy filterEnergy windowTemp.Temp. min.Temp. max.Beam tiltElectron doseOther detailsDate
Side entry liquid nitrogen-cooled cryo specimen holderGATAN LIQUID NITROGEN0.0°0.0° eV90.0 K K K0.0 mrad20 e/Å2
Processing
Software:EMPFT, POR, P3DR
CTF correction:CTF correction included phase and amplitude correction for whole micrographs
Resolution by author:7.9 Å
Resolution method:FSC at 0.5
Unit cell:
Scanned images:
Num. imagesSampling sizeOD rangeQuant. bit numberOther detailsScanner
157 μm/pixel8linkZEISS SCAI
Fitting:
PDBProtocolTarget crit.SoftwareB valueFitting spacePDB chainDetails
1YXN Rigid Bodycorrelation of laplacian filtered data for SITUS, and for EMFIT, target maximizes positive density around an atom, minimizes negative density, and minimizes clashes with neighboring oleculesSITUS and EMFITREALThe fitted molecule consists of two domains, an HK97-like domain and a bacterial immunoglobulin group 2-like domain (BIG2). The two domains were fitted separately.
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