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Crystal structures of spleen tyrosine kinase in complex with a novel inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XG2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 10-20% PEG 3350, 100mM Tris-HCl, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.09 41.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.155 α = 79.83 b = 42.013 β = 90.78 c = 87.66 γ = 79.6
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 RIGAKU JUPITER 210 2011-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0000 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.13 30 94.3 0.069 16.5 2.04 28936
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.13 2.17 82.4 0.284 2.3 1.9 1260
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 MOLECULAR REPLACEMENT THROUGHOUT 4XG2 2.14 30 27485 1451 94.02 0.23903 0.23793 0.2436 0.25989 0.2598 RANDOM 40.694
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] -1.37 1.58 0.17 2.84 -1.36 -1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.034 r_dihedral_angle_4_deg 22.131 r_dihedral_angle_3_deg 17.187 r_dihedral_angle_1_deg 6.689 r_long_range_B_refined 4.842 r_long_range_B_other 4.833 r_mcangle_it 2.907 r_mcangle_other 2.906 r_scangle_other 2.856 r_mcbond_it 1.746
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.034 r_dihedral_angle_4_deg 22.131 r_dihedral_angle_3_deg 17.187 r_dihedral_angle_1_deg 6.689 r_long_range_B_refined 4.842 r_long_range_B_other 4.833 r_mcangle_it 2.907 r_mcangle_other 2.906 r_scangle_other 2.856 r_mcbond_it 1.746 r_mcbond_other 1.746 r_scbond_it 1.687 r_scbond_other 1.686 r_angle_refined_deg 1.657 r_angle_other_deg 1.063 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 4249 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing