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Crystal structure of the dengue virus serotype 3 envelope protein domain III in complex with the variable domains of Mab 4E11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UZG 1UZG, 3UZQ experimental model PDB 3UZQ 1UZG, 3UZQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 20% PEG 8000, 0.1M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.01 38.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.055 α = 90 b = 74.67 β = 104.49 c = 86.888 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M Dynamically bendable mirror 2008-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0721 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.037 42.857 94.8 0.084 10.8 3.5 40602 40602 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.15 76 0.444 0.444 1.7 2.5 4750
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1UZG, 3UZQ 2.04 40.8 40459 40459 1981 94.62 0.2185 0.2185 0.2177 0.2236 0.2338 0.2414 RANDOM 37.2848
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] -2.8499 2.2582 2.1541 0.6959
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.57 t_omega_torsion 2.31 t_angle_deg 0.96 t_bond_d 0.007 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.57 t_omega_torsion 2.31 t_angle_deg 0.96 t_bond_d 0.007 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 Atoms Number Protein Atoms 4816 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 65
Software Software Software Name Purpose SCALA data scaling BUSTER-TNT refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction PHASER phasing BUSTER refinement