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Crystal structure of the kinase domain of TRAF2 and NCK-interacting protein kinase with NCB-0846
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 0.2M Ammonium sulfate
0.1M Bis-tris (5.6)
15% PEG3350
7% Ethyleneglycol
Crystal Properties Matthews coefficient Solvent content 3.13 60.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 212.62 α = 90 b = 124.972 β = 96.32 c = 49.897 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 MARMOSAIC 225 mm CCD 2015-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.0 SPring-8 BL26B2
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 2.9 46.92 100 0.117 15.8 7.7 28803
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 2.9 3.08 100 2.7 7.8
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2X7F 2.9 46.92 1.35 28789 1426 99.95 0.1868 0.1842 0.2391 0.2051
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 13.972 f_angle_d 0.822 f_chiral_restr 0.032 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6915 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 99
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing