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Design and Synthesis of a pan-JAK kinase inhibitor clinical candidate (PF-06263276) suitable for the treatment of inflammatory diseases of the lungs and skin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TJC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1 M Hepes, pH 7.5, 0.1 M Sodium acetate, 30% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.32 46.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.854 α = 90 b = 182.726 β = 110.41 c = 52.766 γ = 90
Symmetry Space Group P 1 21 1
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 2008-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 1 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.69 40 92 0.12 11.9 2.5 16600
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3TJC 2.69 34.54 15717 858 90.93 0.21921 0.2164 0.2169 0.27086 0.2717 RANDOM 36.719
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 0.22 0.71 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.548 r_dihedral_angle_3_deg 18.423 r_dihedral_angle_4_deg 18.005 r_dihedral_angle_1_deg 10.159 r_long_range_B_other 7.246 r_long_range_B_refined 7.228 r_scangle_other 3.862 r_mcangle_it 3.766 r_mcangle_other 3.766 r_scbond_other 2.394
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.548 r_dihedral_angle_3_deg 18.423 r_dihedral_angle_4_deg 18.005 r_dihedral_angle_1_deg 10.159 r_long_range_B_other 7.246 r_long_range_B_refined 7.228 r_scangle_other 3.862 r_mcangle_it 3.766 r_mcangle_other 3.766 r_scbond_other 2.394 r_scbond_it 2.372 r_mcbond_it 2.309 r_mcbond_other 2.307 r_angle_refined_deg 1.571 r_angle_other_deg 0.82 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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 4599 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing