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Crystal structure of IRAK4 kinase domain complexed with AMPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OIB PDB ENTRY 2OIB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 2.3M sodium malonate, 0.1M sodium acetate, 0.01M DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.7 54.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.116 α = 90 b = 138.973 β = 126.43 c = 89.198 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 200 CCD ADSC QUANTUM 315 2005-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.97943 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.3 50 99.9 0.112 8.9 63527 3 50.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION DIFFERENCE FOURIER THROUGHOUT PDB ENTRY 2OIB 2.3 49.94 60299 3217 99.35 0.24381 0.24096 0.29542 RANDOM 53.347
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] 2.63 0.75 -2.31 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.911 r_dihedral_angle_4_deg 19.372 r_dihedral_angle_3_deg 17.344 r_dihedral_angle_1_deg 5.663 r_scangle_it 2.453 r_scbond_it 1.511 r_angle_refined_deg 1.366 r_mcangle_it 1.24 r_mcbond_it 0.711 r_symmetry_hbond_refined 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.911 r_dihedral_angle_4_deg 19.372 r_dihedral_angle_3_deg 17.344 r_dihedral_angle_1_deg 5.663 r_scangle_it 2.453 r_scbond_it 1.511 r_angle_refined_deg 1.366 r_mcangle_it 1.24 r_mcbond_it 0.711 r_symmetry_hbond_refined 0.51 r_symmetry_vdw_refined 0.341 r_nbtor_refined 0.299 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8518 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling