3BQC

High pH-value crystal structure of emodin in complex with the catalytic subunit of protein kinase CK2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293Protein 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 coefficientSolvent content
1.9837.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.87α = 90
b = 45.74β = 111.78
c = 63.5γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2007-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7BEMBL/DESY, HAMBURGBW7B

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.534.399.10.0360.03635.33.7501755015920.4
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)RedundancyNumber Unique Reflections (All)
1.51.5598.80.6070.6071.92.74973

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1pjk1.534.265015947602255798.840.133240.133240.129850.19734RANDOM20.929
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]
-0.610.320.87-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.663
r_dihedral_angle_4_deg21.333
r_dihedral_angle_3_deg13.113
r_scangle_it7.173
r_scbond_it5.74
r_dihedral_angle_1_deg5.681
r_mcangle_it5.558
r_mcbond_it4.889
r_mcbond_other2.283
r_angle_refined_deg1.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.663
r_dihedral_angle_4_deg21.333
r_dihedral_angle_3_deg13.113
r_scangle_it7.173
r_scbond_it5.74
r_dihedral_angle_1_deg5.681
r_mcangle_it5.558
r_mcbond_it4.889
r_mcbond_other2.283
r_angle_refined_deg1.39
r_angle_other_deg0.93
r_symmetry_vdw_other0.321
r_nbd_refined0.223
r_nbd_other0.199
r_nbtor_refined0.185
r_symmetry_hbond_refined0.173
r_xyhbond_nbd_refined0.164
r_symmetry_vdw_refined0.132
r_chiral_restr0.089
r_nbtor_other0.085
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms2828
Nucleic Acid Atoms
Solvent Atoms300
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling