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Crystal structure of dengue 2 virus envelope glycoprotein in complex with the Fab fragment of the broadly neutralizing human antibody EDE1 C8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KDM PDB ENTRIES 3KDM AND 3EYF experimental model PDB 3EYF PDB ENTRIES 3KDM AND 3EYF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 100MM TRIS PH 8.5, 18% (W/V) PEG 8000, 200MM LI2SO4
Crystal Properties Matthews coefficient Solvent content 3.05 0.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.657 α = 90 b = 191.342 β = 90 c = 203.663 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 2013-09-07 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 30 96.2 0.13 7.9 4.5 45639 88.84
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 3.11 97.6 1.01 1.2 4.6
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 ENTRIES 3KDM AND 3EYF 3 19.97 45462 2306 95.57 0.2145 0.2128 0.2358 0.2477 0.2789 RANDOM 88.63
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] 3.2844 -16.861 13.5766
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.91 t_omega_torsion 3.28 t_angle_deg 1.27 t_bond_d 0.01 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 20.91 t_omega_torsion 3.28 t_angle_deg 1.27 t_bond_d 0.01 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 12491 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 120
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing