3Q04

Crystal structure of the apo-form of human CK2 alpha at pH 8.5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PVR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529330% PEG 4000, 0.2M lithium sulfate, 0.1M TrisHCl, pH 8.5, vapor diffusion, sitting drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0439.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.686α = 90
b = 46.065β = 111.51
c = 63.675γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2008-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97625ESRFID23-1

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
11.859.2499.70.0670.06717.53.52950529505
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.999.80.3970.3970.4670.2451.53.64263

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 REPLACEMENTTHROUGHOUT2PVR1.859.2329490149899.60.16450.16170.2163RANDOM21.505
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]
-0.530.190.520.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.774
r_dihedral_angle_4_deg23.397
r_dihedral_angle_3_deg14.662
r_dihedral_angle_1_deg5.82
r_scangle_it5.15
r_scbond_it3.411
r_mcangle_it2.05
r_angle_refined_deg1.915
r_mcbond_it1.25
r_chiral_restr0.149
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.774
r_dihedral_angle_4_deg23.397
r_dihedral_angle_3_deg14.662
r_dihedral_angle_1_deg5.82
r_scangle_it5.15
r_scbond_it3.411
r_mcangle_it2.05
r_angle_refined_deg1.915
r_mcbond_it1.25
r_chiral_restr0.149
r_bond_refined_d0.024
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2773
Nucleic Acid Atoms
Solvent Atoms253
Heterogen Atoms19

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ProDCdata collection
PHASERphasing