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Crystal structure of tyrosine-protein kinase SYK with an inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 10-20% (v/v) PEG 3350, 100mM Tris-HCl (pH 8.5)
, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.12 42.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.964 α = 90 b = 88.281 β = 91.48 c = 40.85 γ = 90
Symmetry Space Group P 1 21 1
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 2011-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 1.0000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.83 50 97 24171
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.86 97.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.83 44.14 22930 1210 97.03 0.21375 0.21189 0.2221 0.24869 0.2585 RANDOM 32.173
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] -0.26 -0.8 -1.33 1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.716 r_dihedral_angle_4_deg 17.258 r_dihedral_angle_3_deg 14.5 r_long_range_B_refined 6.435 r_long_range_B_other 6.342 r_dihedral_angle_1_deg 6.027 r_scangle_other 4.034 r_mcangle_it 3.358 r_mcangle_other 3.357 r_scbond_it 2.473
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.716 r_dihedral_angle_4_deg 17.258 r_dihedral_angle_3_deg 14.5 r_long_range_B_refined 6.435 r_long_range_B_other 6.342 r_dihedral_angle_1_deg 6.027 r_scangle_other 4.034 r_mcangle_it 3.358 r_mcangle_other 3.357 r_scbond_it 2.473 r_scbond_other 2.472 r_mcbond_other 2.178 r_mcbond_it 2.177 r_angle_refined_deg 1.48 r_angle_other_deg 0.836 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 2188 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 31
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling