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Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with Leucettinib-92
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 3350
Crystal Properties Matthews coefficient Solvent content 3.13 60.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.3 α = 90 b = 127.3 β = 90 c = 124.471 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 2023-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999999 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.45 45.05 100 0.999 15.1 13.4 38222
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.55 0.858
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 2.45 45.05 36238 1922 99.95 0.21122 0.20883 0.2167 0.25499 0.2624 RANDOM 60.478
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] 3 3 -5.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.408 r_dihedral_angle_2_deg 14.183 r_long_range_B_other 10.34 r_long_range_B_refined 10.332 r_scangle_other 8.732 r_mcangle_it 7.388 r_mcangle_other 7.388 r_dihedral_angle_1_deg 6.84 r_scbond_it 6.726 r_scbond_other 6.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.408 r_dihedral_angle_2_deg 14.183 r_long_range_B_other 10.34 r_long_range_B_refined 10.332 r_scangle_other 8.732 r_mcangle_it 7.388 r_mcangle_other 7.388 r_dihedral_angle_1_deg 6.84 r_scbond_it 6.726 r_scbond_other 6.484 r_mcbond_it 5.457 r_mcbond_other 5.456 r_angle_refined_deg 1.567 r_angle_other_deg 0.56 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 5415 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing