3UZV

Crystal structure of the dengue virus serotype 2 envelope protein domain III in complex with the variable domains of Mab 4E11


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5292JBS Classic 8 solution D1 (30% ethanol, 12% PEG 6K and 0.1M sodium acetate) diluted 70% in H20, pH 6.5, vapor diffusion, sitting drop, temperature 292K
Crystal Properties
Matthew coefficientSolvent content
2.3647.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.46α = 90
b = 60.46β = 90
c = 207.46γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MDynamically bendable mirror2008-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0721SLSX06SA

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
12.145.598.30.04623.58.12289322893-353.06
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)
12.12.297.50.5643.38.2

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3UZQ, 1OAN2.145.522288022880114697.520.20610.20610.20560.2144RANDOM60.9344
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]
-5.2445-5.244510.4891
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion17.45
t_omega_torsion2.58
t_angle_deg0.97
t_bond_d0.007
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_trig_c_planes
t_utility_distance
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion17.45
t_omega_torsion2.58
t_angle_deg0.97
t_bond_d0.007
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_trig_c_planes
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
t_dihedral_angle_d
t_gen_planes
t_it
t_sum_occupancies
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2524
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms3

Software

Software
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction
SCALAdata scaling
PHASERphasing
BUSTERrefinement