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Crystal structure of the TYK2 pseudokinase domain in complex with compound 11
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 43.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.209 α = 90 b = 112.715 β = 90 c = 157.448 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 2018-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9999 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 1.71 91.65 99.2 0.071 0.085 11.32 3.2 92953
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 1.71 1.96 99.2 0.447 0.536 2.96 3.3
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 1.71 47.62 89919 3022 99.22 0.19115 0.19004 0.1986 0.22541 0.2336 RANDOM 21.303
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] -0.39 0.93 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.998 r_dihedral_angle_4_deg 17.87 r_dihedral_angle_3_deg 11.942 r_dihedral_angle_1_deg 6.153 r_long_range_B_refined 5.025 r_long_range_B_other 4.787 r_angle_refined_deg 1.426 r_angle_other_deg 1.367 r_mcangle_it 1.298 r_mcangle_other 1.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.998 r_dihedral_angle_4_deg 17.87 r_dihedral_angle_3_deg 11.942 r_dihedral_angle_1_deg 6.153 r_long_range_B_refined 5.025 r_long_range_B_other 4.787 r_angle_refined_deg 1.426 r_angle_other_deg 1.367 r_mcangle_it 1.298 r_mcangle_other 1.298 r_scangle_other 1.193 r_mcbond_it 0.729 r_mcbond_other 0.725 r_scbond_it 0.72 r_scbond_other 0.72 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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 6203 Nucleic Acid Atoms Solvent Atoms 671 Heterogen Atoms 135
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing