1OK8

Crystal structure of the dengue 2 virus envelope glycoprotein in the postfusion conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OAMPDB ENTRY 1OAM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1720-30% PEG 400, 0.08 M NACL, 0.1 M MOPS PH 7-8.
Crystal Properties
Matthews coefficientSolvent content
2.44549

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.151α = 90
b = 76.151β = 90
c = 130.775γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2003-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-CAPS14-BM-C

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
1250950.0582572867711.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.07750.39821.2

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 1OAM229.29274501322910.2220.2220.267RANDOM30.1
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]
1.492.181.49-2.98
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d26.4
c_scangle_it6.41
c_scbond_it4.76
c_mcangle_it4.22
c_mcbond_it3.29
c_angle_deg1.4
c_improper_angle_d0.82
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d26.4
c_scangle_it6.41
c_scbond_it4.76
c_mcangle_it4.22
c_mcbond_it3.29
c_angle_deg1.4
c_improper_angle_d0.82
c_bond_d0.006
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 Atoms2962
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms15

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSphasing
CNSrefinement