3G7T

Crystal structure of dengue virus type 1 envelope protein in the postfusion conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OK8PDB entry 1OK8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.528912.5% PEG 550 MME, 0.1 M MES pH 6.5, 10 mM ZnSO4, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.7855.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.65α = 90
b = 75.65β = 90
c = 292.802γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Kohzu HLD*-24 monchromator followed by vertical and horizontal focusing mirrors2007-07-20MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 315Pt-coated toroidal Si mirror for horizontal and vertical focussing followed by double flat Si crystal monochromator2007-08-25MSINGLE WAVELENGTH
1,21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97949APS24-ID-C
2SYNCHROTRONNSLS BEAMLINE X250.97949NSLSX25

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
1,23.55098.70.22312.16794679473.8
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)
1,23.53.63920.7831.647.1607

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1OK83.5256786678631198.320.2120.2080.297RANDOM63.849
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]
-4.11-2.06-4.116.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg46.066
r_dihedral_angle_3_deg26.037
r_dihedral_angle_4_deg16.424
r_scangle_it13.366
r_mcangle_it11.621
r_dihedral_angle_1_deg9.401
r_scbond_it8.8
r_mcbond_it7.201
r_angle_refined_deg1.688
r_chiral_restr0.114
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg46.066
r_dihedral_angle_3_deg26.037
r_dihedral_angle_4_deg16.424
r_scangle_it13.366
r_mcangle_it11.621
r_dihedral_angle_1_deg9.401
r_scbond_it8.8
r_mcbond_it7.201
r_angle_refined_deg1.688
r_chiral_restr0.114
r_bond_refined_d0.018
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2905
Nucleic Acid Atoms
Solvent Atoms1
Heterogen Atoms1

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling