3VBR

Crystal structure of formaldehyde treated empty human Enterovirus 71 particle (room temperature)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VBOPDB ENTRY 3VBO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293200 mM Ammonium phosphate monobasic, 24% (v/v) Isopropanol and 100 mM sodium cacodylate (pH 6.5), VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 354.9α = 90
b = 354.9β = 90
c = 354.9γ = 90
Symmetry
Space GroupP 42 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS PILATUS 6M2011-06-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.96860DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.85092.60.4372.13.169774-1.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.83.9493.80.53.26944

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3VBO3.849.76786467590.30.2570.2570.284RANDOM113.5
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.7
c_scangle_it17.86
c_scbond_it13.27
c_mcangle_it11.11
c_mcbond_it7.16
c_angle_deg1.5
c_improper_angle_d1.02
c_bond_d0.009
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.7
c_scangle_it17.86
c_scbond_it13.27
c_mcangle_it11.11
c_mcbond_it7.16
c_angle_deg1.5
c_improper_angle_d1.02
c_bond_d0.009
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5397
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
GDAdata collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing