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Low 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 3BQC PDB entry 3BQC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 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 ammonium acetate, 0.1M sodium citrate, pH 5.6
Crystallization drop: 2 microliters protein/emodin mixture plus 1 microliter reservoir solution, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.97 37.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.73 α = 90 b = 45.68 β = 111.8 c = 63.24 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 2007-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.9537 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 1.95 19.7 99.9 0.112 0.112 13.9 4.5 22799 22776 25.1
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 1.95 2.02 100 0.626 0.626 2 4.5 2247
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3BQC 1.95 19.7 22776 21615 1161 99.67 0.1877 0.1877 0.18522 0.23346 0.2952 RANDOM 24.78
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] -3.39 0.37 3.52 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.282 r_dihedral_angle_4_deg 18.86 r_dihedral_angle_3_deg 14.57 r_dihedral_angle_1_deg 5.963 r_scangle_it 4.748 r_mcangle_it 4.315 r_mcbond_it 3.833 r_scbond_it 3.674 r_angle_refined_deg 1.397 r_mcbond_other 1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.282 r_dihedral_angle_4_deg 18.86 r_dihedral_angle_3_deg 14.57 r_dihedral_angle_1_deg 5.963 r_scangle_it 4.748 r_mcangle_it 4.315 r_mcbond_it 3.833 r_scbond_it 3.674 r_angle_refined_deg 1.397 r_mcbond_other 1.31 r_angle_other_deg 0.918 r_symmetry_vdw_other 0.264 r_nbd_refined 0.215 r_nbd_other 0.196 r_symmetry_hbond_refined 0.192 r_nbtor_refined 0.19 r_xyhbond_nbd_refined 0.179 r_symmetry_vdw_refined 0.136 r_nbtor_other 0.089 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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 2773 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling