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Tetragonal Complex Structure of Protein Kinase CK2 Catalytic Subunit with a Benzotriazole-Based Inhibitor Generated by click-chemistry
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NGA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 Protein solution: 6 mg/ml CK2alpha, 1 mM Inhibitor, 10 %(v/v) DMSO, 250 mM NaCl, 12.5 mM Tris/HCl, pH 8.5; Reservoir: 25 %(w/v) PEG 3350, 0.2 M Lithiumsulfate, 0.1 M Bis-Tris/HCl, pH 5.5; drop: 1 Mikroliter pre-incubated CK2alpha/Inhibitor solution and 1 Mikroliter reservoir
Crystal Properties Matthews coefficient Solvent content 3.2 61.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.092 α = 90 b = 127.092 β = 90 c = 126.836 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M-F 2012-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.65 44.93 100 0.14 0.14 13.1 7.4 30832
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.79 100 1.173 1.173 2 4.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3NGA 2.65 44.934 1.38 30757 1547 99.92 0.1847 0.1824 0.185 0.2287 0.2247 Random
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 12.261 f_angle_d 0.584 f_chiral_restr 0.025 f_bond_d 0.002 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5586 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 131
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHENIX phasing