3FQE | pdb_00003fqe

Crystal structure of spleen tyrosine kinase complexed with YM193306


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XBBPDB ENTRY 1XBB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.528328% PEG 4000, 0.2M AMMONIUM SULFATE, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
2.2545.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.782α = 90
b = 84.974β = 90
c = 90.148γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.11.0000ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.54593.70.158.74.41082648.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.59680.5281.93743

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1XBB2.5451023451596.840.202760.200190.20.253130.25RANDOM28.146
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]
-0.45-1.531.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.035
r_dihedral_angle_4_deg21.589
r_dihedral_angle_3_deg15.469
r_dihedral_angle_1_deg5.447
r_scangle_it2.054
r_scbond_it1.234
r_angle_refined_deg1.158
r_mcangle_it0.958
r_mcbond_it0.575
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.035
r_dihedral_angle_4_deg21.589
r_dihedral_angle_3_deg15.469
r_dihedral_angle_1_deg5.447
r_scangle_it2.054
r_scbond_it1.234
r_angle_refined_deg1.158
r_mcangle_it0.958
r_mcbond_it0.575
r_nbtor_refined0.301
r_nbd_refined0.188
r_symmetry_vdw_refined0.149
r_xyhbond_nbd_refined0.146
r_chiral_restr0.074
r_symmetry_hbond_refined0.04
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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 Atoms2193
Nucleic Acid Atoms
Solvent Atoms53
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing