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Structural and Thermodynamic Characterization of the TYK2 and JAK3 Kinase Domains in Complex with CP-690550 and CMP-6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YVJ PDB entry 1YVJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 20% PEG-3350, 0.2 M Ammonium Sulfate, 0.02% Phenylurea, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.14 42.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.77 α = 90 b = 75.339 β = 90 c = 88.392 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 200 IMAGE PLATE MAR scanner 300 mm plate M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.5418 APS 21-ID-D
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 2 22.05 97 0.032 44.7 6.5 20521 1 2
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) 2 2.05 0.25 9.2 6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1YVJ 2 22.05 20521 1101 97.43 0.20465 0.20151 0.26478 0.252 RANDOM 22.089
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] 0.05 0.01 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.747 r_dihedral_angle_4_deg 16.449 r_dihedral_angle_3_deg 13.224 r_dihedral_angle_1_deg 7.088 r_scangle_it 2.358 r_scbond_it 1.598 r_angle_refined_deg 1.301 r_mcangle_it 1.21 r_angle_other_deg 1.028 r_mcbond_it 0.761
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.747 r_dihedral_angle_4_deg 16.449 r_dihedral_angle_3_deg 13.224 r_dihedral_angle_1_deg 7.088 r_scangle_it 2.358 r_scbond_it 1.598 r_angle_refined_deg 1.301 r_mcangle_it 1.21 r_angle_other_deg 1.028 r_mcbond_it 0.761 r_symmetry_vdw_other 0.292 r_nbd_refined 0.216 r_nbd_other 0.194 r_nbtor_refined 0.178 r_chiral_restr 0.177 r_symmetry_vdw_refined 0.169 r_symmetry_hbond_refined 0.167 r_xyhbond_nbd_refined 0.137 r_mcbond_other 0.127 r_nbtor_other 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2209 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 23
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling