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Crystal structure of human IL-18 complexed to murine reference antibody 125-2H Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FNS PDB ENTRY 1FNS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 IL-18 AND 125-2H FAB WERE MIXED (1:3 MASS RATIO), INCUBATED OVERNIGHT AT 277 K, PURIFIED BY MONOQ ANION EXCHANGE CHROMATOGRAPHY, AND CONCENTRATED TO 10 MG/ML. THE COMPLEX WAS CRYSTALLIZED BY HANGING DROP VAPOR DIFFUSION BY MIXING COMPLEX (1.5 MICROLITERS [UL]) WITH 1.8 UL OF RESERVOIR SOLUTION (30% PEG 4000, 100 MM TRIS, PH 8.5, 0.2 M MGCL2) AND 0.3 UL OF 300 MM SULFO-BETAINE 201, AND SUSPENDING THE DROP OVER THE RESERVOIR AT 291 K. ROD-LIKE CRYSTALS APPEARED WITHIN ONE WEEK.
Crystal Properties Matthews coefficient Solvent content 2.2 44.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.345 α = 90 b = 62.435 β = 100.39 c = 104.734 γ = 90
Symmetry Space Group P 1 21 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 CCD MARRESEARCH MIRRORS 2003-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 32-ID APS 32-ID
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 1.49 50 94.8 0.06 10.4 3.5 86865 2 21
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 1.49 1.54 56.6 0.35 2.3 2.1
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 1FNS 1.49 31.16 82477 4364 95.5 0.164 0.162 0.1716 0.196 0.204 RANDOM 17.54
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] 0.36 0.84 -0.33 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.698 r_dihedral_angle_4_deg 14.176 r_dihedral_angle_3_deg 12.001 r_dihedral_angle_1_deg 6.85 r_scangle_it 3.508 r_scbond_it 2.562 r_angle_refined_deg 1.662 r_mcangle_it 1.522 r_mcbond_it 1.277 r_angle_other_deg 0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.698 r_dihedral_angle_4_deg 14.176 r_dihedral_angle_3_deg 12.001 r_dihedral_angle_1_deg 6.85 r_scangle_it 3.508 r_scbond_it 2.562 r_angle_refined_deg 1.662 r_mcangle_it 1.522 r_mcbond_it 1.277 r_angle_other_deg 0.92 r_symmetry_vdw_other 0.235 r_nbd_refined 0.219 r_nbd_other 0.199 r_symmetry_hbond_refined 0.188 r_nbtor_refined 0.178 r_symmetry_vdw_refined 0.164 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.103 r_nbtor_other 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4485 Nucleic Acid Atoms Solvent Atoms 593 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing