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Crystal structure of the kinase domain of human TRAF2 and NCK-interacting protein kinase in complex with compund 9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X7F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 24% PEG3350, 0.2M ammonium sulfate,
0.1M Bis-tris (5.6)
Crystal Properties Matthews coefficient Solvent content 2.18 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.178 α = 90 b = 123.204 β = 90 c = 157.652 γ = 90
Symmetry Space Group P 2 21 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 CCD RAYONIX MX-225 2014-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.4 48.54 100 0.131 12.2 7.2 36951
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 100 2.9 7.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2X7F 2.4 48.538 1.35 36883 1851 99.92 0.2079 0.2045 0.2714 0.258 Random selection
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 15.222 f_angle_d 0.982 f_chiral_restr 0.039 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6711 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 103
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing