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Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with 4-(6-((5-isopropoxy-2-methoxyphenyl)amino)pyrazin-2-yl)benzoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Z83
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 293 0.2 M ammonia sulphate
0.1 M bis-tris pH 5.5
23-26% PEG 335
Crystal Properties Matthews coefficient Solvent content 3.18 61.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.968 α = 90 b = 127.968 β = 90 c = 125.127 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 PIXEL DECTRIS EIGER X 16M 2023-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000000 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.6 45.28 99.9 0.204 0.212 0.059 0.998 10.9 13.2 32597
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.72 99.9 2.785 2.893 0.777 0.765 13.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.6 45.28 30917 1595 99.85 0.21313 0.21119 0.2156 0.25095 0.2568 RANDOM 69.725
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] 1.48 1.48 -2.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.733 r_long_range_B_other 7.916 r_long_range_B_refined 7.915 r_dihedral_angle_2_deg 7.762 r_scangle_other 6.787 r_dihedral_angle_1_deg 6.455 r_mcangle_it 5.38 r_mcangle_other 5.379 r_scbond_other 4.666 r_scbond_it 4.665
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.733 r_long_range_B_other 7.916 r_long_range_B_refined 7.915 r_dihedral_angle_2_deg 7.762 r_scangle_other 6.787 r_dihedral_angle_1_deg 6.455 r_mcangle_it 5.38 r_mcangle_other 5.379 r_scbond_other 4.666 r_scbond_it 4.665 r_mcbond_it 3.577 r_mcbond_other 3.576 r_angle_refined_deg 1.447 r_angle_other_deg 0.542 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5315 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing