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Crystal structure of A259C covalently linked dengue 2 virus envelope glycoprotein dimer 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 4UTA 4UTA;4UT7 experimental model PDB 4UT7 4UTA;4UT7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 100mM Hepes pH 7.5, 19% PEG 6K, 1.5% (v/v) 2-methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.77 55.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.774 α = 90 b = 182.301 β = 90 c = 208.725 γ = 90
Symmetry Space Group P 2 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 173 PIXEL DECTRIS EIGER X 9M 2015-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.984 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 3.9 50 96.9 0.316 0.316 0.41 0.257 3.1 3.8 19112 44.52
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.9 4.1 97.5 0.8 0.67 0.68 1.4 3.8
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 4UTA;4UT7 3.9 20 19112 947 90.67 0.2861 0.2854 0.3244 0.3 0.3637 RANDOM 145.06
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] 9.7707 -67.7068 57.9362
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.67 t_omega_torsion 2.88 t_angle_deg 1.13 t_bond_d 0.007 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 20.67 t_omega_torsion 2.88 t_angle_deg 1.13 t_bond_d 0.007 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 9701 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 142
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling