3LM5

Crystal Structure of human Serine/Threonine Kinase 17B (STK17B) in complex with Quercetin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EHAPDB entry 3EHA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52770.2M NaCl; 0.1M BIS-TRIS pH 5.5; 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6854.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.38α = 90
b = 83.38β = 90
c = 115.3γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR2252009-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.98DiamondI02

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
12.2952.4993.20.0970.09712.56.618152
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.292.391000.9020.9022.26.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 3EHA2.2952.49166011660189491.690.204010.200110.28081RANDOM18.239
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]
0.540.54-1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.17
r_dihedral_angle_4_deg19.689
r_dihedral_angle_3_deg14.064
r_scangle_it10.466
r_scbond_it9.754
r_mcangle_it7.133
r_mcbond_it5.641
r_dihedral_angle_1_deg5.511
r_mcbond_other2.282
r_angle_refined_deg1.457
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.17
r_dihedral_angle_4_deg19.689
r_dihedral_angle_3_deg14.064
r_scangle_it10.466
r_scbond_it9.754
r_mcangle_it7.133
r_mcbond_it5.641
r_dihedral_angle_1_deg5.511
r_mcbond_other2.282
r_angle_refined_deg1.457
r_angle_other_deg0.875
r_chiral_restr0.083
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2185
Nucleic Acid Atoms
Solvent Atoms118
Heterogen Atoms22

Software

Software
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling