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Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with allosteric compound FG5
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 60.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.648 α = 90 b = 127.648 β = 90 c = 123.901 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 2023-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99999 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 2.25 45.17 100 0.999 16.9 13.4 49160
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 2.25 2.32 0.778 1.8
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 2.25 45.17 46690 2399 99.97 0.2098 0.20764 0.2142 0.25252 0.2592 RANDOM 53.18
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] 2.11 2.11 -4.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.454 r_dihedral_angle_2_deg 13.539 r_scangle_other 7.731 r_dihedral_angle_1_deg 6.382 r_mcangle_it 5.84 r_mcangle_other 5.84 r_scbond_it 5.773 r_scbond_other 5.515 r_mcbond_it 4.335 r_mcbond_other 4.334
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.454 r_dihedral_angle_2_deg 13.539 r_scangle_other 7.731 r_dihedral_angle_1_deg 6.382 r_mcangle_it 5.84 r_mcangle_other 5.84 r_scbond_it 5.773 r_scbond_other 5.515 r_mcbond_it 4.335 r_mcbond_other 4.334 r_angle_refined_deg 1.52 r_angle_other_deg 0.574 r_chiral_restr 0.086 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 5500 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 193
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing