☰ Navigation Tabs
Crystal Structure of IRAK4 kinase in complex with a small molecule inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NRU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 298 0.1 M sodium acetate pH 5.4, 2.3 M sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.49 50.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.63 α = 90 b = 140.802 β = 127.64 c = 86.496 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 IMAGE PLATE RIGAKU 2010-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-002+ 1.5
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.14 100 89.9 0.095 0.76 2.4 2.4 21131
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.14 3.21 86.8 0.38 0.75 2.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2NRU 3.2 29.62 18229 977 89.22 0.2662 0.2614 0.2483 0.355 0.3432 RANDOM 34.886
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] -0.2 -0.16 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.013 r_dihedral_angle_4_deg 17.424 r_dihedral_angle_3_deg 16.452 r_dihedral_angle_1_deg 5.947 r_angle_refined_deg 1.134 r_angle_other_deg 0.718 r_symmetry_hbond_refined 0.393 r_nbd_refined 0.213 r_symmetry_vdw_other 0.197 r_xyhbond_nbd_refined 0.189
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.013 r_dihedral_angle_4_deg 17.424 r_dihedral_angle_3_deg 16.452 r_dihedral_angle_1_deg 5.947 r_angle_refined_deg 1.134 r_angle_other_deg 0.718 r_symmetry_hbond_refined 0.393 r_nbd_refined 0.213 r_symmetry_vdw_other 0.197 r_xyhbond_nbd_refined 0.189 r_nbd_other 0.17 r_symmetry_vdw_refined 0.166 r_nbtor_other 0.081 r_xyhbond_nbd_other 0.074 r_chiral_restr 0.055 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9323 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling AMoRE phasing