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Crystal structure of dengue 2 virus envelope glycoprotein in complex with the Fab fragment of the broadly neutralizing human antibody EDE2 A11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H0T PDB ENTRY 3H0T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 100MM HEPES PH 7.5 10% (W/V) PEG 6,000 5% (V/V) MPD
Crystal Properties Matthews coefficient Solvent content 2.82 0.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.779 α = 90 b = 181.85 β = 90 c = 204.823 γ = 90
Symmetry Space Group P 21 21 21
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 2013-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 3.85 50 98.3 0.27 5.8 4.83 21168 68.58
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 3.85 4.22 98.3 0.92 1.4 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 PDB ENTRY 3H0T 3.85 20 21007 1070 97.88 0.2311 0.2297 0.2777 0.2567 0.2948 RANDOM 129.32
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] -11.3483 -26.0736 37.4219
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.63 t_omega_torsion 3.04 t_angle_deg 1.18 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.63 t_omega_torsion 3.04 t_angle_deg 1.18 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 12517 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 194
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing