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High pH-value crystal structure of emodin in complex with the catalytic subunit of protein kinase CK2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PJK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Protein stock solution: 10mg/ml protein in 500mM NaCl, 25mM Tris/HCl, pH 8.5
Emodin stock solution: 10mM in water
Protein/emodin mixture: equal volumes of protein and emodin stock solutions were mixed and equillibrated for 30 min prior to crystallization
Reservoir: 30% PEG4000, 0.2M lithium sulfate, 0.1M Tris/HCl, pH 8.5
Crystallization drop: 2 mikroliters protein/emodin mixture plus 1 mikroliter reservoir solution, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.98 37.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.87 α = 90 b = 45.74 β = 111.78 c = 63.5 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 IMAGE PLATE MAR scanner 345 mm plate 2007-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
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 1.5 34.3 99.1 0.036 0.036 35.3 3.7 50175 50159 20.4
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) 1.5 1.55 98.8 0.607 0.607 1.9 2.7 4973
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 1pjk 1.5 34.26 50159 47602 2557 98.84 0.13324 0.13324 0.12985 0.2051 0.19734 0.2506 RANDOM 20.929
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] -0.61 0.32 0.87 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.663 r_dihedral_angle_4_deg 21.333 r_dihedral_angle_3_deg 13.113 r_scangle_it 7.173 r_scbond_it 5.74 r_dihedral_angle_1_deg 5.681 r_mcangle_it 5.558 r_mcbond_it 4.889 r_mcbond_other 2.283 r_angle_refined_deg 1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.663 r_dihedral_angle_4_deg 21.333 r_dihedral_angle_3_deg 13.113 r_scangle_it 7.173 r_scbond_it 5.74 r_dihedral_angle_1_deg 5.681 r_mcangle_it 5.558 r_mcbond_it 4.889 r_mcbond_other 2.283 r_angle_refined_deg 1.39 r_angle_other_deg 0.93 r_symmetry_vdw_other 0.321 r_nbd_refined 0.223 r_nbd_other 0.199 r_nbtor_refined 0.185 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.164 r_symmetry_vdw_refined 0.132 r_chiral_restr 0.089 r_nbtor_other 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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 2828 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling