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Crystal structure of spleen tyrosine kinase complexed with R406
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XBB PDB ENTRY 1XBB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 283 24% PEG 4000, 0.2M AMMONIUM SULFATE, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.29 46.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.971 α = 90 b = 85.079 β = 90 c = 91.144 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 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 2.1 45 87 0.14 9.1 4.7 16386 33.4
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 2.1 2.18 55.3 0.51 1.8 4.3 1013
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1XBB 2.1 42.52 15501 839 86.89 0.21791 0.21608 0.2141 0.25327 0.2573 RANDOM 41.749
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] -3.1 -2.84 5.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.221 r_dihedral_angle_4_deg 19.365 r_dihedral_angle_3_deg 13.931 r_dihedral_angle_1_deg 5.173 r_scangle_it 1.922 r_scbond_it 1.243 r_angle_refined_deg 1.064 r_mcangle_it 0.887 r_mcbond_it 0.524 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.221 r_dihedral_angle_4_deg 19.365 r_dihedral_angle_3_deg 13.931 r_dihedral_angle_1_deg 5.173 r_scangle_it 1.922 r_scbond_it 1.243 r_angle_refined_deg 1.064 r_mcangle_it 0.887 r_mcbond_it 0.524 r_nbtor_refined 0.304 r_nbd_refined 0.185 r_symmetry_vdw_refined 0.159 r_symmetry_hbond_refined 0.157 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 Atoms Number Protein Atoms 2184 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement CNS refinement ADSC data collection DENZO data reduction SCALEPACK data scaling CNS phasing