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Structure of the IL-18 Surrogate Cytokine Agonist DR3087
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6B20
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.1 M MES pH 6.0
1.6 M Magnesium sulfate
Crystal Properties Matthews coefficient Solvent content 4.18 70.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.807 α = 90 b = 172.658 β = 90.01 c = 59.292 γ = 90
Symmetry Space Group C 1 2 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 EIGER X 16M 2023-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.979 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.4 37.7 95.6 0.055 0.064 0.033 0.999 11.8 3.7 34359
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 97.1 0.788 0.921 0.473 0.784 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.4 37.7 32612 1697 95.35 0.24328 0.24144 0.2475 0.28043 0.2889 RANDOM 72.856
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] 9.55 0.14 -5.08 -4.47
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 15.051 r_long_range_B_other 15.049 r_dihedral_angle_3_deg 14.983 r_scangle_other 11.279 r_mcangle_it 11.264 r_mcangle_other 11.264 r_dihedral_angle_2_deg 9.636 r_dihedral_angle_1_deg 8.656 r_mcbond_it 7.702 r_mcbond_other 7.702
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 15.051 r_long_range_B_other 15.049 r_dihedral_angle_3_deg 14.983 r_scangle_other 11.279 r_mcangle_it 11.264 r_mcangle_other 11.264 r_dihedral_angle_2_deg 9.636 r_dihedral_angle_1_deg 8.656 r_mcbond_it 7.702 r_mcbond_other 7.702 r_scbond_it 7.542 r_scbond_other 7.54 r_angle_refined_deg 1.718 r_angle_other_deg 0.584 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3486 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ISOLDE model building Coot model building Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction