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Human CK2 catalytic domain in complex with a difurane derivative inhibitor (CPA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PJK PDB ENTRY 1PJK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 36 % polyethylene glycol 5000 monomethyl ether, 150 mM ammonium sulphate and 100 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.01 38.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.776 α = 90 b = 45.787 β = 111.65 c = 63.673 γ = 90
Symmetry Space Group P 1 21 1
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 2007-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 1.0722 ESRF ID23-2
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 1.75 19.84 97.1 0.05 0.05 17.2 3.6 31145 31145
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.75 1.81 86.9 0.408 0.408 2.9 3.6 2646
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1PJK 1.75 19.77 28558 28558 3174 100 0.18621 0.18153 0.22887 0.2261 RANDOM 24.854
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.521 r_dihedral_angle_4_deg 19.256 r_dihedral_angle_3_deg 14.753 r_dihedral_angle_1_deg 6.091 r_scangle_it 2.46 r_mcangle_it 2.295 r_scbond_it 1.659 r_angle_refined_deg 1.485 r_mcbond_it 1.417 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.521 r_dihedral_angle_4_deg 19.256 r_dihedral_angle_3_deg 14.753 r_dihedral_angle_1_deg 6.091 r_scangle_it 2.46 r_mcangle_it 2.295 r_scbond_it 1.659 r_angle_refined_deg 1.485 r_mcbond_it 1.417 r_chiral_restr 0.093 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 2782 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 27
Software Software Software Name Purpose AMoRE phasing REFMAC refinement XDS data reduction XDS data scaling