☰ Navigation Tabs
Complex structure of human protein kinase CK2 catalytic subunit with a thieno[2,3-d]pyrimidin inhibitor crystallized under high-salt conditions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NSZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 Protein stock solution: 6 mg/ml CK2alpha1-335 in 0.5 M NaCl, 25 mM Tris/HCl, pH 8.5;
Inhibitor stock solution: 10 mM inhibitor in DMSO;
Protein/inhibitor complex solution: 90 microliter protein stock solution + 10 microliter inhibitor stock solution;
Reservoir solution: 4.2 M NaCl, 0.1 M sodium citrate, pH 5.0;
Drop solution before equlibration: 0.5 microliter protein/inhibitor complex solution + 0.5 microliter reservoir solution
Crystal Properties Matthews coefficient Solvent content 2.13 42.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.061 α = 90 b = 72.061 β = 90 c = 131.579 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 IMAGE PLATE MARRESEARCH 2012-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.71 28 100 0.131 0.131 0.996 15.75 6.9 9935 38.9
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 2.71 2.807 98 0.8084 0.693 2.32 5.9
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3NSZ 2.71 27.841 1.36 9935 956 99.78 0.2225 0.2186 0.2179 0.2593 0.2592
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 17.009 f_angle_d 0.535 f_chiral_restr 0.04 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2782 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 27
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing