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Inactive conformation of human protein kinase CK2 catalytic subunit
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: 10mg/ml CK2alpha, 500mM sodium chloride, 25mM Tris/HCl, pH 8.5;
Reservoir: 2M ammonium sulfate, 2M sodium chloride;
Drop: 0.001mL reservoir solution, 0.001mL protein stock solution, 0.003mL 1mM AMPPNP, 0.0006mL 10mM magnesium chloride, 0.0001mL glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.99 38.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.324 α = 90 b = 71.324 β = 90 c = 125.681 γ = 90
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 MARMOSAIC 225 mm CCD 2007-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.95370 EMBL/DESY, HAMBURG X12
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 2.3 34.5 96.9 0.1 0.1 17.6 7.7 27863 26999 47.1
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 2.3 2.38 98.3 0.724 2 7.2
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 (All) 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 2.3 34.3 27046 25746 1253 96.9 0.17256 0.17256 0.16969 0.1753 0.23272 0.1742 RANDOM 41.145
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] 7.87 7.87 -15.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.377 r_dihedral_angle_4_deg 15.562 r_dihedral_angle_3_deg 15.173 r_dihedral_angle_1_deg 4.734 r_mcangle_it 2.556 r_scangle_it 2.175 r_mcbond_it 1.612 r_scbond_it 1.558 r_angle_refined_deg 0.885 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.377 r_dihedral_angle_4_deg 15.562 r_dihedral_angle_3_deg 15.173 r_dihedral_angle_1_deg 4.734 r_mcangle_it 2.556 r_scangle_it 2.175 r_mcbond_it 1.612 r_scbond_it 1.558 r_angle_refined_deg 0.885 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5634 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 28
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling