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Crystal structure of murine NF-kappaB inducing kinase (NIK) bound to a 6-alkynylindoline (cmp1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G3C apo murine NIK kinase domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 277 2uL protein with 2uL well solution of 0.5 M ammonium sulfate, 0.9 M lithium sulfate,0.1M sodium citrate tribasic dihydrate then soaked in well solution with 1 mM cmp1, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.98 58.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.145 α = 90 b = 143.145 β = 90 c = 45.151 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD ADSC QUANTUM 315 2012-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.97946 SSRL BL7-1
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 2.5 50 99.6 0.068 18.6 3.7 32116 32116 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 100 0.598 2 3.7 3153
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 apo murine NIK kinase domain 2.5 47.73 32110 32110 3259 99.54 0.19446 0.19446 0.18931 0.1831 0.24047 0.2353 RANDOM 45.801
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] -0.28 -0.28 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.37 r_dihedral_angle_4_deg 18.466 r_dihedral_angle_3_deg 16.331 r_dihedral_angle_1_deg 5.697 r_angle_refined_deg 1.224 r_chiral_restr 0.08 r_bond_refined_d 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4956 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 69
Software Software Software Name Purpose Web-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling