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Crystal structure of the Fab fragment of anti-IL-6 antibody I9H
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YK4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100 mM Tris-HCl, 20% PEG 20000
Crystal Properties Matthews coefficient Solvent content 3.42 64.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.36 α = 90 b = 126.36 β = 90 c = 143.36 γ = 120
Symmetry Space Group P 62 2 2
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 APEX II CCD 2016-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER IMUS MICROFOCUS 1.542
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 2.5 47.8 97.1 0.06 0.99 10.7 23.8 23296 42.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.56 84.7 1.766 0.131 0.4 2.3
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 FREE R-VALUE 4YK4 2.5 47.79 1.33 22927 1965 95.54 0.2603 0.258 0.2641 0.2847 0.2902 46.65
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 14.0061 f_angle_d 0.587 f_chiral_restr 0.0419 f_plane_restr 0.0042 f_bond_d 0.0022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3338 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 19
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement