3Q9W

Crystal structure of human CK2 alpha in complex with emodin at pH 8.5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PVRPDB ENTRY 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
1.9336.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.337α = 90
b = 45.619β = 111.88
c = 62.613γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2008-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.972937ESRFID29

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
11.758.12490.30.0620.06214.32.73055130551
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)
11.71.7958.10.3050.3050.4080.2671.91.82836

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 2PVR1.758.1230538153190.170.1730.17030.2234RANDOM19.736
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]
-0.550.230.610.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.928
r_dihedral_angle_4_deg20.715
r_dihedral_angle_3_deg14.799
r_dihedral_angle_1_deg6.228
r_scangle_it4.824
r_scbond_it3.196
r_angle_refined_deg2.032
r_mcangle_it1.997
r_mcbond_it1.217
r_chiral_restr0.135
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.928
r_dihedral_angle_4_deg20.715
r_dihedral_angle_3_deg14.799
r_dihedral_angle_1_deg6.228
r_scangle_it4.824
r_scbond_it3.196
r_angle_refined_deg2.032
r_mcangle_it1.997
r_mcbond_it1.217
r_chiral_restr0.135
r_bond_refined_d0.023
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2773
Nucleic Acid Atoms
Solvent Atoms291
Heterogen Atoms35

Software

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