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Crystal structure of pro-interleukin-18 and caspase-4 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6KMZ caspase-4 experimental model PDB 2VXT IL-18 experimental model PDB 7WR2 OspC3 ARD domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.2 M Calcium acetate, 0.1M Tris-HCl pH 9.0, 13% PEG 8000, 0.01 M L-Glutathione reduced, 0.01 M L-Glutathione oxidized
Crystal Properties Matthews coefficient Solvent content 2.97 58.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.254 α = 90 b = 86.254 β = 90 c = 194.12 γ = 120
Symmetry Space Group P 31 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 EIGER2 S 9M 2022-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
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 3.12 74.7 100 0.113 0.119 0.035 0.999 16 11.1 15561 101.19
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 3.12 3.29 100 1.312 0.41 0.71 2.6 11.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 3.12 59.2 1.34 15497 1551 99.84 0.2411 0.2378 0.2377 0.2693 0.2694 107.01
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 12.3327 f_angle_d 0.5503 f_chiral_restr 0.044 f_bond_d 0.0038 f_plane_restr 0.0038
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4269 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing