6ZJF

Crystal structure of STK17B (DRAK2) in complex with AP-229


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LM0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6277.1519% PEG 3350, 0.1M NaCl, 0.1M bis-tris 6.0
Crystal Properties
Matthews coefficientSolvent content
2.6653.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.349α = 90
b = 83.349β = 90
c = 114.259γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)1.03320PETRA III, EMBL c/o DESYP13 (MX1)

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
11.7537.271000.0840.0960.0360.99811.97.241311
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)
11.751.811000.8650.9980.3610.5092.17.4

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 REPLACEMENTTHROUGHOUT3LM01.7537.2739226203699.910.18090.17940.21RANDOM31.099
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]
-0.37-0.370.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.859
r_dihedral_angle_4_deg22.326
r_dihedral_angle_3_deg13.6
r_dihedral_angle_1_deg6.57
r_angle_refined_deg1.496
r_angle_other_deg1.381
r_chiral_restr0.089
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.859
r_dihedral_angle_4_deg22.326
r_dihedral_angle_3_deg13.6
r_dihedral_angle_1_deg6.57
r_angle_refined_deg1.496
r_angle_other_deg1.381
r_chiral_restr0.089
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2358
Nucleic Acid Atoms
Solvent Atoms231
Heterogen Atoms35

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing