7A3Q

Crystal structure of dengue 4 virus envelope glycoprotein in complex with the scFv fragment of the broadly neutralizing human antibody EDE1 C10


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UAJ3UAJ, 3FKU
experimental modelPDB 3FKU3UAJ, 3FKU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION291100 mM CAPSO pH 9.6, 16.7% (w/v) PEG 8,000, 200 mM NaCl
Crystal Properties
Matthews coefficientSolvent content
2.7455.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.985α = 90
b = 133.18β = 92.15
c = 93.536γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2013-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 11.254SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.74099.10.99812.53.1943980
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.899.10.6881.2

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 REPLACEMENTTHROUGHOUT3UAJ, 3FKU2.72043818220499.010.21710.2160.2387RANDOM81.58
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]
0.8694-3.6286-2.46011.5907
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion18.79
t_omega_torsion1.91
t_angle_deg0.93
t_bond_d0.007
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion18.79
t_omega_torsion1.91
t_angle_deg0.93
t_bond_d0.007
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9351
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms58

Software

Software
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing
XDSdata reduction