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Crystal structure of the dengue virus serotype 2 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 3UZQ 3UZQ, 1OAN experimental model PDB 1OAN 3UZQ, 1OAN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292 JBS 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 Matthews coefficient Solvent content 2.36 47.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.46 α = 90 b = 60.46 β = 90 c = 207.46 γ = 90
Symmetry Space Group P 41 21 2
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 Merge 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 2.1 45.5 98.3 0.046 23.5 8.1 22893 22893 -3 53.06
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.2 97.5 0.564 3.3 8.2
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 3UZQ, 1OAN 2.1 45.52 22880 22880 1146 97.52 0.2061 0.2061 0.2056 0.2123 0.2144 0.2214 RANDOM 60.9344
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 -5.2445 10.4891
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.45 t_omega_torsion 2.58 t_angle_deg 0.97 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 17.45 t_omega_torsion 2.58 t_angle_deg 0.97 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 2524 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 3
Software Software Software Name Purpose BUSTER-TNT refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction SCALA data scaling PHASER phasing BUSTER refinement