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Structure of a human CK2alpha prime, the paralog isoform of the catalytic subunit of protein kinase CK2 from Homo sapiens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PVR PDB ENTRY 2PVR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Protein stock solution: 6 mg/ml protein, 25 mM Tris/HCl, pH 8.5, 500 mM sodium chloride, 1 mM inhibitor 3-(4,5,6,7-tetrabromo-1H-benzotriazol-1-yl)propan-1-ol
Reservoir: 28 % PEG6000, 500 mM lithium chloride, 100 mM Tris/HCl, pH 8.5
Drop: mixture of 0.5 uL protein solution plus 0.5 uL reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.52 51.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.69 α = 112.4 b = 47.57 β = 89.49 c = 50.57 γ = 91.3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2009-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 33.03 86.8 0.057 0.057 12.61 2.2 27265 23663 -3 26.083
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 47.7 0.257 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 2PVR 2 33.03 27265 22479 1184 86.8 0.17378 0.17197 0.1784 0.20721 0.2095 RANDOM 26.698
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] 1.01 -0.2 0.34 -0.26 -1.11 -1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.102 r_dihedral_angle_4_deg 14.052 r_dihedral_angle_3_deg 11.425 r_dihedral_angle_1_deg 5.1 r_scangle_it 4.127 r_scbond_it 2.89 r_mcangle_it 2.208 r_mcbond_it 1.46 r_angle_refined_deg 0.975 r_angle_other_deg 0.776
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.102 r_dihedral_angle_4_deg 14.052 r_dihedral_angle_3_deg 11.425 r_dihedral_angle_1_deg 5.1 r_scangle_it 4.127 r_scbond_it 2.89 r_mcangle_it 2.208 r_mcbond_it 1.46 r_angle_refined_deg 0.975 r_angle_other_deg 0.776 r_mcbond_other 0.591 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2749 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 18
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling