3JUH

Crystal structure of a mutant of human protein kinase CK2alpha with altered cosubstrate specificity


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52932.2M sodium citrate, 2mM AMPPNP, 4mM magnesium chloride, 0.62mM peptide RRRADDSDDDDD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0138.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.368α = 90
b = 71.368β = 90
c = 126.467γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2004-01-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.811EMBL/DESY, HAMBURGX13

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
11.6639.597.50.05817.515.17468372782-330.398
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)
11.661.782.40.522.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.6639.4570535223997.340.158210.156280.2184RANDOM25.858
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]
-3.32-3.326.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.971
r_dihedral_angle_4_deg23.42
r_dihedral_angle_3_deg17.439
r_dihedral_angle_1_deg7.369
r_angle_refined_deg2.148
r_angle_other_deg1.12
r_chiral_restr0.13
r_bond_refined_d0.024
r_mcbond_it0.018
r_mcbond_other0.015
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.971
r_dihedral_angle_4_deg23.42
r_dihedral_angle_3_deg17.439
r_dihedral_angle_1_deg7.369
r_angle_refined_deg2.148
r_angle_other_deg1.12
r_chiral_restr0.13
r_bond_refined_d0.024
r_mcbond_it0.018
r_mcbond_other0.015
r_gen_planes_refined0.011
r_bond_other_d0.003
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_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5630
Nucleic Acid Atoms
Solvent Atoms518
Heterogen Atoms80

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction