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Structure of protein kinase CK2 catalytic subunit in complex with the CK2beta-competitive bisubstrate inhibitor ARC1502
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PVR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1 microliter of the CK2alpha/ARC1502 mixture (composition: 7 mg/ml CK2alpha enzyme, 1 mM ARC1502, 10 % dimethyl sulfoxide, 450 mM NaCl, 25 mM Tris/HCl, pH 8.5) was mixed with 2.5 mikroliter reservoir solution (composition: 30 % PEG4000, 0.2 M ammonium acetate, 0.1 M sodium citrate, pH 5.6) followed by vapour diffusion equilibration against 100 microliter of the reservoir solution.
Crystal Properties Matthews coefficient Solvent content 1.99 38.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.761 α = 90 b = 45.717 β = 110.69 c = 63.727 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 2M-F 2012-10-20 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) 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 1.994 49.723 93.38 0.2085 0.2085 0.967 15.91 4.4 19533 28.54
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.994 2.266 66.25 0.5205 0.5205 0.669 2.76 3.2
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 2PVR 1.994 49.72 1.38 19438 952 90.55 0.1861 0.1841 0.2228 0.2249
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 10.868 f_angle_d 0.894 f_chiral_restr 0.054 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2779 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 80
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing