1PJK

Crystal Structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JWHCHAIN A of PDB ENTRY 1JWH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293PEGmme 5000, ammonium sulfate, MES, adenylyl imidodiphosphate, magnesium chloride, peptide RRRADDSDDDDD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0539.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.044α = 90
b = 46.502β = 112.02
c = 64.262γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray283IMAGE PLATEMARRESEARCHOsmic mirrors2002-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.517.398.50.1188.42.3112071120741.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5999.9

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 REPLACEMENTTHROUGHOUTCHAIN A of PDB ENTRY 1JWH2.517.31009910099110098.510.187920.187920.180270.25737RANDOM12.728
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]
-1.11.05-1.523.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.064
r_scangle_it1.605
r_angle_refined_deg1.119
r_scbond_it0.938
r_angle_other_deg0.769
r_mcangle_it0.769
r_mcbond_it0.411
r_symmetry_vdw_other0.224
r_nbd_other0.206
r_nbd_refined0.182
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.064
r_scangle_it1.605
r_angle_refined_deg1.119
r_scbond_it0.938
r_angle_other_deg0.769
r_mcangle_it0.769
r_mcbond_it0.411
r_symmetry_vdw_other0.224
r_nbd_other0.206
r_nbd_refined0.182
r_symmetry_hbond_refined0.182
r_xyhbond_nbd_refined0.166
r_symmetry_vdw_refined0.13
r_nbtor_other0.082
r_chiral_restr0.068
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_xyhbond_nbd_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2793
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing