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Crystal structure of the catalytic subunit of human protein kinase CK2 with 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 1.5M ammonium sulfate, 0.2M tri-sodium citrate, 0.2M K/Na tartrate pH 5.6, the enzyme was preincubated with 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.01 38.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.506 α = 90 b = 71.506 β = 90 c = 125.789 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 CCD MARMOSAIC 225 mm CCD 2006-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.9 EMBL/DESY, HAMBURG X12
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.56 25 99.9 89590 89486
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.56 25 89590 87584 1860 99.91 0.15666 0.15666 0.15578 0.1953 0.19811 0.2293 RANDOM 23.844
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] -1.02 -1.02 2.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.235 r_dihedral_angle_3_deg 13.674 r_dihedral_angle_4_deg 13.665 r_dihedral_angle_1_deg 5.708 r_scangle_it 4.01 r_scbond_it 3.211 r_mcangle_it 2.495 r_mcbond_it 1.948 r_angle_refined_deg 1.189 r_mcbond_other 0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.235 r_dihedral_angle_3_deg 13.674 r_dihedral_angle_4_deg 13.665 r_dihedral_angle_1_deg 5.708 r_scangle_it 4.01 r_scbond_it 3.211 r_mcangle_it 2.495 r_mcbond_it 1.948 r_angle_refined_deg 1.189 r_mcbond_other 0.92 r_angle_other_deg 0.84 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 5667 Nucleic Acid Atoms Solvent Atoms 617 Heterogen Atoms 92
Software Software Software Name Purpose MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling