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Structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit with the ATP-competitive inhibitor resorufin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NGA PDB ENTRY 3NGA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 293 reservoir:
30 % polyethylene glycol 8000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate buffer;
drop:
2 microliters preincubated CK2alpha/resorufin mixture (5 mM resorufin, 5 mg/ml Ck2alpha), 1 reservoir solution , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.2 61.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.777 α = 90 b = 127.777 β = 90 c = 125.766 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 CCD MAR CCD 165 mm 2008-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 3.2 38.5 99.6 0.178 0.178 14.6 10.2 17653
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 3.2 3.37 100 0.689 0.689 3.9 10.4
Refinement Statistics Diffraction ID Structure Solution 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 PDB ENTRY 3NGA 3.2 19.948 1.36 17632 881 99.89 0.2024 0.2008 0.2009 0.2311 0.2268
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] 0.871 0.871 -1.7421
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.877 f_angle_d 0.574 f_chiral_restr 0.044 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5586 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 98
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling