2OXD

Protein kinase CK2 in complex with tetrabromobenzoimidazole K17, K22 and K32 inhibitors


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZOEPDB entry 1ZOE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829310-20% PEG 4000, 0.2 M sodium acetate, 0.1 M TrisHCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.4549.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.148α = 90
b = 60.316β = 103.56
c = 46.238γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.369.1788.50.0911.81.9168501491322
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.32.4292.70.2162.81.82268

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1ZOE2.369.171102557786.930.223380.220720.2733RANDOM35.988
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]
-2.78-1.890.141.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.57
r_dihedral_angle_4_deg18.35
r_dihedral_angle_3_deg15.456
r_dihedral_angle_1_deg5.912
r_scangle_it1.662
r_angle_refined_deg1.325
r_scbond_it1.137
r_mcangle_it0.856
r_mcbond_it0.507
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.57
r_dihedral_angle_4_deg18.35
r_dihedral_angle_3_deg15.456
r_dihedral_angle_1_deg5.912
r_scangle_it1.662
r_angle_refined_deg1.325
r_scbond_it1.137
r_mcangle_it0.856
r_mcbond_it0.507
r_nbtor_refined0.304
r_symmetry_vdw_refined0.24
r_symmetry_hbond_refined0.212
r_nbd_refined0.207
r_xyhbond_nbd_refined0.187
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 AtomsNumber
Protein Atoms2713
Nucleic Acid Atoms
Solvent Atoms79
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing