3H30

Crystal structure of the catalytic subunit of human protein kinase CK2 with 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52931.5M ammonium sulfate, 0.2M tri-sodium citrate, 0.2M K/Na tartrate pH 5.6, the enzyme was preincubated with 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0138.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.506α = 90
b = 71.506β = 90
c = 125.789γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARMOSAIC 225 mm CCD2006-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X120.9EMBL/DESY, HAMBURGX12

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.562599.98959089486

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.56258959087584186099.910.156660.156660.155780.19811RANDOM23.844
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]
-1.02-1.022.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.235
r_dihedral_angle_3_deg13.674
r_dihedral_angle_4_deg13.665
r_dihedral_angle_1_deg5.708
r_scangle_it4.01
r_scbond_it3.211
r_mcangle_it2.495
r_mcbond_it1.948
r_angle_refined_deg1.189
r_mcbond_other0.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.235
r_dihedral_angle_3_deg13.674
r_dihedral_angle_4_deg13.665
r_dihedral_angle_1_deg5.708
r_scangle_it4.01
r_scbond_it3.211
r_mcangle_it2.495
r_mcbond_it1.948
r_angle_refined_deg1.189
r_mcbond_other0.92
r_angle_other_deg0.84
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms5667
Nucleic Acid Atoms
Solvent Atoms617
Heterogen Atoms92

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling