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Crystal structure of spleen tyrosine kinase complexed with 2-(3,4,5-Trimethoxy-phenyl)-5H-pyrrolo[2,3-b]pyrazine-7-carboxylic acid isopropylamide
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 28% PEG4000, 0.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.25 45.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.785 α = 90 b = 85.118 β = 90 c = 90.158 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 ADSC QUANTUM 315r M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0000 ALS 5.0.2
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 45.08 99 0.055 17.3 4.9 18234 39.4
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 95.3 0.513 1.9 3.9 1710
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 1XBB 2.1 45.08 17258 931 98.46 0.23682 0.23499 0.27151 0.2932 RANDOM 49.59
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 -2.71 2.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.782 r_dihedral_angle_4_deg 16.477 r_dihedral_angle_3_deg 14.239 r_dihedral_angle_1_deg 4.99 r_scangle_it 2.048 r_scbond_it 1.331 r_angle_refined_deg 1.101 r_mcangle_it 0.926 r_mcbond_it 0.565 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.782 r_dihedral_angle_4_deg 16.477 r_dihedral_angle_3_deg 14.239 r_dihedral_angle_1_deg 4.99 r_scangle_it 2.048 r_scbond_it 1.331 r_angle_refined_deg 1.101 r_mcangle_it 0.926 r_mcbond_it 0.565 r_nbtor_refined 0.301 r_nbd_refined 0.18 r_symmetry_vdw_refined 0.137 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.097 r_symmetry_hbond_refined 0.097 r_bond_refined_d 0.009 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 2152 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement CNS refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing