3C13

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BQCPDB entry 3BQC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.6293Protein 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 coefficientSolvent content
1.9737.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.73α = 90
b = 45.68β = 111.8
c = 63.24γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X120.9537EMBL/DESY, HAMBURGX12

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
11.9519.799.90.1120.11213.94.5227992277625.1
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)RedundancyNumber Unique Reflections (All)
11.952.021000.6260.62624.52247

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 REPLACEMENTTHROUGHOUTPDB entry 3BQC1.9519.72277621615116199.670.18770.18770.185220.23346RANDOM24.78
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]
-3.390.373.520.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.282
r_dihedral_angle_4_deg18.86
r_dihedral_angle_3_deg14.57
r_dihedral_angle_1_deg5.963
r_scangle_it4.748
r_mcangle_it4.315
r_mcbond_it3.833
r_scbond_it3.674
r_angle_refined_deg1.397
r_mcbond_other1.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.282
r_dihedral_angle_4_deg18.86
r_dihedral_angle_3_deg14.57
r_dihedral_angle_1_deg5.963
r_scangle_it4.748
r_mcangle_it4.315
r_mcbond_it3.833
r_scbond_it3.674
r_angle_refined_deg1.397
r_mcbond_other1.31
r_angle_other_deg0.918
r_symmetry_vdw_other0.264
r_nbd_refined0.215
r_nbd_other0.196
r_symmetry_hbond_refined0.192
r_nbtor_refined0.19
r_xyhbond_nbd_refined0.179
r_symmetry_vdw_refined0.136
r_nbtor_other0.089
r_chiral_restr0.087
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.001
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 Atoms2773
Nucleic Acid Atoms
Solvent Atoms300
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling