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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 8 293 10% Ethanol, 0.1 M Tris, 0.3 M magnesium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.96 37.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.306 α = 90 b = 74.262 β = 90 c = 106.46 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 CCD MARMOSAIC 300 mm CCD mirrors 2009-07-07 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 2.5 18.6 99.7 0.068 31.87 6 10002 10002 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.56 100 0.102 0.19 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB entry 1YVJ 2.5 18.58 10002 10002 502 99.6 0.2233 0.22021 0.2211 0.28637 0.2887 RANDOM 15.63
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] 0.19 -0.15 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.183 r_dihedral_angle_4_deg 20.479 r_dihedral_angle_3_deg 18.891 r_dihedral_angle_1_deg 9.547 r_scangle_it 1.87 r_angle_refined_deg 1.405 r_angle_other_deg 1.3 r_scbond_it 1.189 r_mcangle_it 1.081 r_mcbond_it 0.626
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.183 r_dihedral_angle_4_deg 20.479 r_dihedral_angle_3_deg 18.891 r_dihedral_angle_1_deg 9.547 r_scangle_it 1.87 r_angle_refined_deg 1.405 r_angle_other_deg 1.3 r_scbond_it 1.189 r_mcangle_it 1.081 r_mcbond_it 0.626 r_symmetry_vdw_other 0.22 r_nbd_refined 0.208 r_nbd_other 0.193 r_nbtor_refined 0.192 r_symmetry_hbond_refined 0.187 r_chiral_restr 0.171 r_xyhbond_nbd_refined 0.146 r_symmetry_vdw_refined 0.117 r_nbtor_other 0.09 r_mcbond_other 0.085 r_bond_refined_d 0.009 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 2238 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 23
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling