4DFN

Crystal structure of spleen tyrosine kinase complexed with an adamantylpyrazine inhibitor


X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.5251.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.295α = 90
b = 84.848β = 90
c = 90.996γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PILATUS 6MDECTRIS2009-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.4862.0699.40.0695.611590
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.482.6497.20.8195.5

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 DIFFRACTIONOTHERTHROUGHOUTNONE2.4862.0611532101899.50.2220.21710.2734RANDOM73.515
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]
0.58-2.912.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.322
r_dihedral_angle_4_deg15.642
r_dihedral_angle_3_deg12.723
r_dihedral_angle_1_deg5.02
r_scangle_it4.529
r_scbond_it3.062
r_mcangle_it2.051
r_mcbond_it1.134
r_angle_refined_deg0.862
r_angle_other_deg0.744
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.322
r_dihedral_angle_4_deg15.642
r_dihedral_angle_3_deg12.723
r_dihedral_angle_1_deg5.02
r_scangle_it4.529
r_scbond_it3.062
r_mcangle_it2.051
r_mcbond_it1.134
r_angle_refined_deg0.862
r_angle_other_deg0.744
r_mcbond_other0.244
r_chiral_restr0.054
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2190
Nucleic Acid Atoms
Solvent Atoms22
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling