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Crystal structure of spleen tyrosine kinase complexed with 3-(8-{4-[Ethyl-(2-hydroxy-ethyl)-amino]-phenylamino}-imidazo[1,2-a]pyrazin-5-yl)-phenol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FQE PDB ENTRY 3FQE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 283 28% PEG 4000, 0.2M ammonium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.28 45.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.958 α = 90 b = 85.112 β = 90 c = 90.752 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 325 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.3 50 87.1 0.18 6.9 5.4 14003 12188 42.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 62 0.574 1.7 3.7 722
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 3FQE 2.318 45.36 11532 614 86.56 0.22795 0.22581 0.26912 0.2873 RANDOM 57.843
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] -4.05 -3.93 7.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.075 r_dihedral_angle_4_deg 16.436 r_dihedral_angle_3_deg 15.908 r_dihedral_angle_1_deg 5.387 r_scangle_it 2.069 r_scbond_it 1.274 r_angle_refined_deg 1.144 r_mcangle_it 0.965 r_mcbond_it 0.55 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.075 r_dihedral_angle_4_deg 16.436 r_dihedral_angle_3_deg 15.908 r_dihedral_angle_1_deg 5.387 r_scangle_it 2.069 r_scbond_it 1.274 r_angle_refined_deg 1.144 r_mcangle_it 0.965 r_mcbond_it 0.55 r_nbtor_refined 0.301 r_nbd_refined 0.196 r_symmetry_hbond_refined 0.182 r_xyhbond_nbd_refined 0.15 r_symmetry_vdw_refined 0.143 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 Atoms Number Protein Atoms 2180 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement CNS refinement ADSC data collection DENZO data reduction SCALEPACK data scaling CNS phasing