4I0R

Crystal structure of spleen tyrosine kinase complexed with 2-(3,4,5-Trimethoxy-phenyl)-5H-pyrrolo[2,3-b]pyrazine-7-carboxylic acid isopropylamide


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% PEG4000, 0.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
2.2545.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.785α = 90
b = 85.118β = 90
c = 90.158γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.0000ALS5.0.2

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
12.145.08990.05517.34.91823439.4
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)
12.12.1895.30.5131.93.91710

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1XBB2.145.081725893198.460.236820.234990.27151RANDOM49.59
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]
0.01-2.712.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.782
r_dihedral_angle_4_deg16.477
r_dihedral_angle_3_deg14.239
r_dihedral_angle_1_deg4.99
r_scangle_it2.048
r_scbond_it1.331
r_angle_refined_deg1.101
r_mcangle_it0.926
r_mcbond_it0.565
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.782
r_dihedral_angle_4_deg16.477
r_dihedral_angle_3_deg14.239
r_dihedral_angle_1_deg4.99
r_scangle_it2.048
r_scbond_it1.331
r_angle_refined_deg1.101
r_mcangle_it0.926
r_mcbond_it0.565
r_nbtor_refined0.301
r_nbd_refined0.18
r_symmetry_vdw_refined0.137
r_xyhbond_nbd_refined0.127
r_chiral_restr0.097
r_symmetry_hbond_refined0.097
r_bond_refined_d0.009
r_gen_planes_refined0.004
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 Atoms2152
Nucleic Acid Atoms
Solvent Atoms80
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing