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Monoclinic 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 2PVR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 Protein solution: 6 mg/ml CK2alpha, 0.44 mM AMPPNP, 0.89 mM magnesium chloride, 250 mM NaCl, 12.5 mM Tris/HCl, pH 8.5; Reservoir: 30%(w/v) PEG4000, 0.2 M Lithiumsulfate, 0.1 M Tris/HCL, pH 8.5; the inhibitor JRJ was introduced by extensive soaking for one week
Crystal Properties Matthews coefficient Solvent content 2.02 39.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.481 α = 90 b = 46.894 β = 111.56 c = 63.464 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 2012-05-06 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 2.35 35.52 99.7 0.12 0.12 13.4 3.3 13511
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 2.35 2.48 98.3 0.372 0.372 2.2 2.7 1936
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 2pvr 2.35 35.516 1.34 13511 668 99.75 0.1988 0.196 0.1968 0.2514 0.2523 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 11.726 f_angle_d 0.512 f_chiral_restr 0.023 f_bond_d 0.002 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2771 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 53
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHENIX phasing