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Crystal structure of human Interleukin-1 receptor associated Kinase 4 (IRAK 4, CID 100300) in complex with compound NCC00371481 (BSI 107591)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NRU PDB entry 2NRU as per Morda
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 289 9.5 mg/ml IRAK4 (CID100300, Batch BOS047020B) in 20 mM Tris-HCl, pH 8.0, 1 mM DTT, with 1 mM BSI107659 (NCGC00371481) in DMSO, crystallization condition: Microlytic screen MCSG1, E10: 0.2 M ammonium tartrate dibasic, 20% PEG3350, cryoprotectant: 20% ethylene glycol with 1 mM compound, tray 286446 e10, puck: xvc2-1
Crystal Properties Matthews coefficient Solvent content 2.57 52.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.29 α = 90 b = 141.91 β = 126.22 c = 87.89 γ = 90
Symmetry Space Group C 1 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 CCD RIGAKU SATURN 944+ RIGAKU VARIMAX 2016-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.1 45.729 98.9 0.09 0.097 0.999 15.89 7.47 79032 24.07
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 96.2 0.433 0.47 0.923 5.1 6.568
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2NRU as per Morda 2.1 45.729 1.34 78992 2041 99.3 0.1682 0.1672 0.1686 0.2066 0.205 0 32.1855
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 16.151 f_angle_d 0.921 f_chiral_restr 0.058 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8976 Nucleic Acid Atoms Solvent Atoms 1011 Heterogen Atoms 124
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MoRDa phasing Coot model building