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Crystal structure of human IL-8 in a large unit cell
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D14
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 0.02 M Magnesium chloride hexahydrate, 0.05 M MOPS pH 7.0, 55% (v/v) Tacsimate pH 7.0, 0.002 M Hexamine cobalt (III) chloride
Crystal Properties Matthews coefficient Solvent content 2.72 54.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.881 α = 90 b = 127.469 β = 90 c = 210.291 γ = 90
Symmetry Space Group C 2 2 21
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 2025-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97920 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.89 70.15 99.9 0.124 0.993 3.4 6.7 48985 43.03
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.93 0.194
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 2.2 63.73 1.34 31073 1573 99.34 0.222 0.2208 0.2206 0.245 0.2453 62.6
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 10.9292 f_angle_d 0.4674 f_chiral_restr 0.0442 f_plane_restr 0.0034 f_bond_d 0.0023
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3448 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing