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Crystal structure of spleen tyrosine kinase complexed with 2-(5,6,7,8-Tetrahydro-imidazo[1,5-a]pyridin-1-yl)-5H-pyrrolo[2,3-b]pyrazine-7-carboxylic acid tert-butylamide
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 2.28 46.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.854 α = 90 b = 87.405 β = 90 c = 88.867 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 RAYONIX MX225HE M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 1.0000 APS 31-ID
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 1.7 43.7 98.74 0.125 10.3 6.7 32809
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 1.7 1.744 98.64 0.583 1.8 6.6 2546
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 1.7 43.7 32809 1739 98.74 0.2359 0.23415 0.2307 0.26799 0.2645 RANDOM 19.16
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] -0.46 -1.04 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.754 r_dihedral_angle_4_deg 23.447 r_dihedral_angle_3_deg 16.798 r_dihedral_angle_1_deg 5.925 r_scangle_it 4.992 r_scbond_it 3.245 r_mcangle_it 2.131 r_angle_refined_deg 1.797 r_mcbond_it 1.278 r_chiral_restr 0.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.754 r_dihedral_angle_4_deg 23.447 r_dihedral_angle_3_deg 16.798 r_dihedral_angle_1_deg 5.925 r_scangle_it 4.992 r_scbond_it 3.245 r_mcangle_it 2.131 r_angle_refined_deg 1.797 r_mcbond_it 1.278 r_chiral_restr 0.138 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2166 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 25
Software Software Software Name Purpose MAR345 data collection REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing