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Crystal structure of the TYK2 pseudokinase domain in complex with compound 8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 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 optimised 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 2.15 42.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.108 α = 90 b = 112.602 β = 90 c = 156.856 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 2017-10-20 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 1.87 91.47 95.2 0.13 0.149 10.92 4.3 68019
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 1.87 2.12 97.2 0.445 0.504 3.55 4.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.87 47.47 65806 2213 95.22 0.22617 0.22454 0.27367 0.2438 RANDOM 21.432
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] 0.66 1.03 -1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.677 r_dihedral_angle_4_deg 15.729 r_dihedral_angle_3_deg 13.234 r_dihedral_angle_1_deg 6.548 r_long_range_B_refined 5.364 r_long_range_B_other 5.216 r_angle_refined_deg 1.778 r_angle_other_deg 1.42 r_mcangle_it 0.933 r_mcangle_other 0.933
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.677 r_dihedral_angle_4_deg 15.729 r_dihedral_angle_3_deg 13.234 r_dihedral_angle_1_deg 6.548 r_long_range_B_refined 5.364 r_long_range_B_other 5.216 r_angle_refined_deg 1.778 r_angle_other_deg 1.42 r_mcangle_it 0.933 r_mcangle_other 0.933 r_scangle_other 0.766 r_mcbond_it 0.514 r_mcbond_other 0.514 r_scbond_it 0.473 r_scbond_other 0.472 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 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 6092 Nucleic Acid Atoms Solvent Atoms 625 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PHASER phasing XDS data reduction