6QF4

X-Ray structure of human Serine/Threonine Kinase 17B (STK17B) aka DRAK2 in complex with ADP obtained by on-chip soaking


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LM5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE7.52950.2M ammonium acetate, 20% PEG 3350, 50mM sodium/potassium tartrate, 0.8mM quercetin
Crystal Properties
Matthews coefficientSolvent content
2.8957.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.479α = 90
b = 85.479β = 90
c = 118.073γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-04-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.0PETRA III, DESYP11

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1fixed target
Fixed Target
Diffraction IDDescriptionSample HoldingSupport BaseMotion controlSample Solvent
1single crystalline silicon chipgoniometer

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
12.49542.7498.60.1070.1130.0360.99714.79.31552941.29
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)
12.52.699.60.4930.5220.1660.9225.39.7

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-VALUE3LM52.49542.7391.3415521155297.920.18710.18270.226857.04
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_d11.772
f_angle_d0.476
f_chiral_restr0.043
f_bond_d0.002
f_plane_restr0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2307
Nucleic Acid Atoms
Solvent Atoms122
Heterogen Atoms58

Software

Software
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHASERphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling
XDSdata reduction