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Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with allosteric ligand FGC3337
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8PVO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.1 M bis-tris pH 5.5
23-26% (v/v) PEG 3350
0.2 M ammonia sulphate
Crystal Properties Matthews coefficient Solvent content 3.16 61.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.158 α = 90 b = 128.158 β = 90 c = 124.014 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 1.000030 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 2.65 48.31 100 0.995 9.8 13.5 30650
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 2.65 2.78 0.755
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.65 45.31 29021 1573 99.96 0.21436 0.21273 0.24473 0.2276 RANDOM 49.465
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] 0.39 0.39 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.43 r_dihedral_angle_2_deg 12.215 r_dihedral_angle_1_deg 6.471 r_long_range_B_refined 6.203 r_long_range_B_other 6.201 r_scangle_other 4.529 r_mcangle_it 3.511 r_mcangle_other 3.511 r_scbond_it 2.99 r_scbond_other 2.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.43 r_dihedral_angle_2_deg 12.215 r_dihedral_angle_1_deg 6.471 r_long_range_B_refined 6.203 r_long_range_B_other 6.201 r_scangle_other 4.529 r_mcangle_it 3.511 r_mcangle_other 3.511 r_scbond_it 2.99 r_scbond_other 2.95 r_mcbond_it 2.172 r_mcbond_other 2.172 r_angle_refined_deg 1.571 r_angle_other_deg 0.59 r_chiral_restr 0.094 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 5440 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 161
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing