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Crystal structure of the TYK2 pseudokinase domain in complex with TAK-279
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298 The purified protein was used in crystallization trials employing both, a standard screen with approximately 1200 different conditions, as well as crystallization conditions identified using literature data. Conditions initially obtained have been optimized using standard strategies, systematically varying parameters critically influencing crystallization, such as temperature, protein concentration, drop ratio, and others. These conditions were also refined by systematically varying pH or precipitant concentrations
Crystal Properties Matthews coefficient Solvent content 2.16 43.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.222 α = 90 b = 112.94 β = 90 c = 157.348 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 PIXEL DECTRIS PILATUS 6M 2018-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0000 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) 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 91.75 96.1 0.055 0.067 15.93 2.9 74066
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 2.08 96.1 0.421 0.514 2.97 2.9
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 45.92 71595 2388 96.37 0.18614 0.18488 0.1922 0.22398 0.2274 RANDOM 25.003
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] -0.86 1.24 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.161 r_dihedral_angle_4_deg 17.904 r_dihedral_angle_3_deg 12.576 r_dihedral_angle_1_deg 6.348 r_long_range_B_refined 5.259 r_long_range_B_other 5.086 r_angle_refined_deg 1.505 r_mcangle_it 1.502 r_mcangle_other 1.502 r_scangle_other 1.485
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.161 r_dihedral_angle_4_deg 17.904 r_dihedral_angle_3_deg 12.576 r_dihedral_angle_1_deg 6.348 r_long_range_B_refined 5.259 r_long_range_B_other 5.086 r_angle_refined_deg 1.505 r_mcangle_it 1.502 r_mcangle_other 1.502 r_scangle_other 1.485 r_angle_other_deg 1.374 r_scbond_it 0.896 r_scbond_other 0.896 r_mcbond_it 0.871 r_mcbond_other 0.847 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 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 6242 Nucleic Acid Atoms Solvent Atoms 596 Heterogen Atoms 178
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing