9FET

Crystal Structure of Human Vaccinia-related kinase 2 (VRK-2) bound to JA-47


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8Q1Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.1520% PEG6000 -- 10% ethylene glycol -- 0.1M tris pH 7.5 -- 0.1M calcium chloride
Crystal Properties
Matthews coefficientSolvent content
2.2545.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.675α = 90
b = 71.314β = 90
c = 158.718γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2022-03-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.918396SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.444.411000.99914.21312986
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.490.8551.7

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.444.411232566099.950.224210.221830.2270.26870.2616RANDOM61.088
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]
-2.557.33-4.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.144
r_dihedral_angle_4_deg15.246
r_dihedral_angle_3_deg15.12
r_long_range_B_refined13.154
r_long_range_B_other13.154
r_mcangle_it8.295
r_mcangle_other8.293
r_scangle_other8.147
r_dihedral_angle_1_deg7.194
r_mcbond_it5.484
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2423
Nucleic Acid Atoms
Solvent Atoms10
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing