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STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA') IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR 4P
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 293 90 MIKROLITER ENZYME STOCK SOLUTION (5
MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 10
MIKROLITER 4P STOCK SOLUTION (10 MM 4P IN DMSO). THIS
MIXTURE WAS INCUBATED FOR 30 MIN AT ROOM TEMPERATURE. THE
RESERVOIR SOLUTION OF THE CRYSTALLIZATION EXPERIMENT WAS 25 % (W/
V) PEG3350, 0.2 M AMMONIUM ACETATE, 0.1 M HEPES BUFFER, PH 8.5.
PRIOR TO EQUILIBRATION THE CRYSTALLIZATION DROP WAS COMPOSED OF
1 MIKROLITER RESERVOIR SOLUTION PLUS 1 MIKROLITER ENZYME/4P
MIXTURE., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.488 α = 90 b = 112.128 β = 90 c = 143.692 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 PILATUS3 6M 2017-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.0000 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.998 71.48 99.69 0.177 0.177 0.999 7.39 6.7 51742 24.98
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 1.998 2.07 97.59 1.191 1.191 0.673 1.41 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1.998 71.48 51726 1041 99.7 0.1748 0.1738 0.1758 0.2211 0.2216
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 14.522 f_angle_d 1.124 f_chiral_restr 0.067 f_bond_d 0.011 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5513 Nucleic Acid Atoms Solvent Atoms 443 Heterogen Atoms 83
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing