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Structure of the IL-18 Surrogate Cytokine Agonist DR3085
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 8.5 293 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5 and 1.26 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 4.25 71.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.64 α = 90 b = 92.64 β = 90 c = 181.846 γ = 120
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 2024-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.979 SSRL BL12-1
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 3.59 39.5 99.3 0.449 0.516 0.251 0.904 3.5 4.1 10210
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 3.59 3.93 98.3 1.109 1.277 0.625 0.655 4
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 3.8 39.2 8208 437 98.99 0.23793 0.23517 0.239 0.29098 0.2933 RANDOM 85.978
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] 2.38 1.19 2.38 -7.72
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 14.203 r_long_range_B_refined 14.202 r_dihedral_angle_3_deg 14.15 r_scangle_other 9.851 r_mcangle_it 9.637 r_mcangle_other 9.635 r_dihedral_angle_1_deg 6.798 r_scbond_it 5.807 r_scbond_other 5.806 r_mcbond_it 5.766
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 14.203 r_long_range_B_refined 14.202 r_dihedral_angle_3_deg 14.15 r_scangle_other 9.851 r_mcangle_it 9.637 r_mcangle_other 9.635 r_dihedral_angle_1_deg 6.798 r_scbond_it 5.807 r_scbond_other 5.806 r_mcbond_it 5.766 r_mcbond_other 5.765 r_dihedral_angle_2_deg 4.473 r_angle_refined_deg 1.283 r_angle_other_deg 0.431 r_chiral_restr 0.05 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 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 3447 Nucleic Acid Atoms Solvent Atoms 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