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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 2.12 42.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.192 α = 90 b = 75.187 β = 90 c = 89.07 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 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 1.74 25.13 100 0.03 47.9 6.9 31422 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) 1.74 1.8 100 0.33 0.33 3.56 6.7
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 1.74 25.13 31422 31422 1678 99.58 0.195 0.1933 0.1999 0.22697 0.2328 RANDOM 21.427
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] 0.06 -0.01 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.287 r_dihedral_angle_4_deg 20.748 r_dihedral_angle_3_deg 12.714 r_dihedral_angle_1_deg 8.24 r_scangle_it 2.869 r_scbond_it 1.832 r_angle_refined_deg 1.364 r_mcangle_it 1.34 r_angle_other_deg 0.986 r_mcbond_it 0.893
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.287 r_dihedral_angle_4_deg 20.748 r_dihedral_angle_3_deg 12.714 r_dihedral_angle_1_deg 8.24 r_scangle_it 2.869 r_scbond_it 1.832 r_angle_refined_deg 1.364 r_mcangle_it 1.34 r_angle_other_deg 0.986 r_mcbond_it 0.893 r_symmetry_vdw_other 0.343 r_nbd_refined 0.226 r_chiral_restr 0.204 r_nbd_other 0.196 r_symmetry_vdw_refined 0.193 r_nbtor_refined 0.182 r_mcbond_other 0.181 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.117 r_nbtor_other 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 2217 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 23
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling