4FF8

Inhibitor bound structure of the kinase domain of the murine receptor tyrosine kinase TYRO3 (Sky)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729517% PEG 3350, 0.1M magnesium nitrate, 0.1 M Bis-Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.2344.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.522α = 90
b = 57.245β = 100.85
c = 60.076γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDADSC QUANTUM 210r2005-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.00APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.245086.315860136872.32.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.242.3226.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.447.671164060795.690.279010.276640.32412RANDOM60.809
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]
-1.32-0.32-1.552.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.564
r_dihedral_angle_4_deg20.049
r_dihedral_angle_3_deg17.208
r_dihedral_angle_1_deg6.246
r_angle_refined_deg1.405
r_scangle_it1.398
r_scbond_it0.947
r_mcangle_it0.808
r_angle_other_deg0.789
r_mcbond_it0.446
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.564
r_dihedral_angle_4_deg20.049
r_dihedral_angle_3_deg17.208
r_dihedral_angle_1_deg6.246
r_angle_refined_deg1.405
r_scangle_it1.398
r_scbond_it0.947
r_mcangle_it0.808
r_angle_other_deg0.789
r_mcbond_it0.446
r_nbtor_refined0.296
r_symmetry_vdw_refined0.192
r_symmetry_hbond_refined0.163
r_xyhbond_nbd_refined0.105
r_chiral_restr0.077
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1363
Nucleic Acid Atoms
Solvent Atoms3
Heterogen Atoms34

Software

Software
Software NamePurpose
ADSCdata collection
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing