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Crystal structure of human interleukin 18 receptor beta extracellular domain in complex with an antagonistic scFv
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WO4 3WO4, 3PNW experimental model PDB 3PNW 3WO4, 3PNW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 288 0.2M Ammonium iodide, 20% polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.5 50.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.16 α = 90 b = 163.16 β = 90 c = 64.145 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 80 PIXEL DECTRIS PILATUS3 6M 2017-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL19U1 0.97775 NFPSS BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.3 50 98.6 0.113 0.134 0.071 7.7 3.4 28309 45.95
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 3.3 3.42 95.3 0.652 0.796 0.45 0.558 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3WO4, 3PNW 3.302 39.19 0.06 24923 1204 86.98 0.2484 0.2469 0.2521 0.2769 0.2792 50.0901
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.271 f_angle_d 1.376 f_chiral_restr 0.063 f_bond_d 0.011 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9712 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 56
Software Software Software Name Purpose PHENIX refinement HKL-3000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing