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ORTHORHOMBIC COMPLEX STRUCTURE OF HUMAN PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA') WITH THE INHIBITOR 4'-CARBOXY-6,8-CHLORO- FLAVONOL (FLC21)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OFM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 PROTEIN STOCK SOLUTION: 5.5 MG/ML CK2ALPHA'D39G-C336S 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: 25 % PEG5000 MME, 0.2 M ammonium sulphate, 0.1 M MES buffer, pH 6.5;
DROP SOLUTION BEFORE EQULIBRATION: 0.3 MICROLITER PROTEIN/INHIBITOR COMPLEX SOLUTION + 0.3 MICROLITER RESERVOIR SOLUTION
Crystal Properties Matthews coefficient Solvent content 3.32 62.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.85 α = 90 b = 83.78 β = 90 c = 142.344 γ = 90
Symmetry Space Group P 21 21 21
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 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 2.195 44.6 99 0.1909 0.1909 0.998 9.99 6.4 29246 21.44
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 2.195 2.274 93 1.185 0.684 1.72 5.6
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 3OFM 2.195 44.502 1.35 28094 1142 99.2 0.1721 0.1704 0.1713 0.214 0.2156
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 15.776 f_angle_d 0.576 f_chiral_restr 0.043 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2785 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 71
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing