5Y5T

Crystal structures of spleen tyrosine kinase in complex with a novel inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4XG2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP27710-20% PEG 3350, 100mM Tris-HCl, pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.0840.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.246α = 90
b = 84.979β = 99.59
c = 42.142γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-05-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)1.0000PAL/PLS5C (4A)

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
11.85093.90.05249.27.0224430
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)
11.81.8354.50.3693.54.6734

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 REPLACEMENTTHROUGHOUT4XG21.842.4923205120093.90.196080.193910.2344RANDOM41.174
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]
-2.18-1.81-1.884.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.655
r_dihedral_angle_4_deg17.962
r_dihedral_angle_3_deg13.213
r_long_range_B_refined7.563
r_long_range_B_other7.52
r_dihedral_angle_1_deg5.864
r_scangle_other4.411
r_mcangle_it4.027
r_mcangle_other4.026
r_scbond_it2.639
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.655
r_dihedral_angle_4_deg17.962
r_dihedral_angle_3_deg13.213
r_long_range_B_refined7.563
r_long_range_B_other7.52
r_dihedral_angle_1_deg5.864
r_scangle_other4.411
r_mcangle_it4.027
r_mcangle_other4.026
r_scbond_it2.639
r_scbond_other2.638
r_mcbond_other2.478
r_mcbond_it2.477
r_angle_refined_deg1.312
r_angle_other_deg0.918
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2150
Nucleic Acid Atoms
Solvent Atoms162
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing