7Q7C

Room temperature structure of the human Serine/Threonine Kinase 17B (STK17B/DRAK2) in complex with ADP at atmospheric pressure


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6QF4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE29520 mg/ml protein in 25 mM HEPES pH 7.5, 500 mM NaCl, 0.5 mM TCEP was mixed 1:1.5 with precipitant solution (0.1 M HEPES 6.5, 0.2M ammonium acetate, 20% PEG 3350, 50mM sodium/potassium tartrate, 0.8mM quercetin). Batch grown crystals were subsequently mixed 1:1 with 100 mM ATP/50mM magnesium chloride in DRAK2 crystallization buffer and incubated for half an hour.
Crystal Properties
Matthews coefficientSolvent content
2.7855.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.44α = 90
b = 84.44β = 90
c = 116.61γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295PIXELDECTRIS PILATUS3 X CdTe 2M2019-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P110.979PETRA III, DESYP11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
22.8547.9898.910.2010.2150.0740.9915.937.81028292.37
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.852.95297.311.0851.1950.4860.4570.995.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6QF42.8547.981.3310271102798.950.21020.20720.237697.15
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d11.9029
f_angle_d0.4802
f_chiral_restr0.0419
f_plane_restr0.0027
f_bond_d0.0023
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2189
Nucleic Acid Atoms
Solvent Atoms6
Heterogen Atoms28

Software

Software
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
PHENIXphasing