3LM0

Crystal Structure of human Serine/Threonine Kinase 17B (STK17B)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EHA3EHA.pdb

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72770.2M (NH4)3(cit)20% PEG 3350, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.754.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.54α = 90
b = 83.54β = 90
c = 115.64γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR2252009-10-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.976DiamondI04

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
12.3552.6199.90.1310.13111.47.217724
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)
12.352.4899.30.750.752.14.9

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 REPLACEMENTTHROUGHOUT3EHA.pdb2.3552.61167951679589699.840.205660.202430.26749RANDOM14.42
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]
-0.52-0.521.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.425
r_dihedral_angle_4_deg20.269
r_dihedral_angle_3_deg14.882
r_dihedral_angle_1_deg6.019
r_scangle_it3.177
r_scbond_it2.025
r_angle_refined_deg1.545
r_mcangle_it1.231
r_angle_other_deg0.926
r_mcbond_it0.661
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.425
r_dihedral_angle_4_deg20.269
r_dihedral_angle_3_deg14.882
r_dihedral_angle_1_deg6.019
r_scangle_it3.177
r_scbond_it2.025
r_angle_refined_deg1.545
r_mcangle_it1.231
r_angle_other_deg0.926
r_mcbond_it0.661
r_mcbond_other0.152
r_chiral_restr0.085
r_bond_refined_d0.016
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 Atoms2207
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms31

Software

Software
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling