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Structure Guided Development of Novel Thymidine Mimetics targeting Pseudomonas aeruginosa Thymidylate Kinase: from Hit to Lead Generation
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 The protein was mixed 1:1 with a reservoir solution containing 30% PEG 4000, 0.2M MgCl2, and 0.1 M Tris pH 7.5 - 8.5 and incubated at 295, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 1.81 31.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.341 α = 90 b = 118.063 β = 90 c = 41.918 γ = 90
Symmetry Space Group P 21 21 2
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 ADSC QUANTUM 210 2010-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-ID
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 1.9 62.87 99.7 0.069 18.7 3.7 29391 110874 2 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) 1 1.9 1.97 100 0.443 2.6 3.7 2876
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.91 62.87 29391 27872 1489 99.45 0.19688 0.19688 0.19455 0.1966 0.2424 0.2445 RANDOM 28.215
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] -0.88 -0.16 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.008 r_dihedral_angle_4_deg 23.638 r_dihedral_angle_1_deg 21.728 r_dihedral_angle_3_deg 16.157 r_scangle_it 6.707 r_scbond_it 4.655 r_mcangle_it 2.98 r_mcbond_it 2.077 r_angle_refined_deg 1.742 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.008 r_dihedral_angle_4_deg 23.638 r_dihedral_angle_1_deg 21.728 r_dihedral_angle_3_deg 16.157 r_scangle_it 6.707 r_scbond_it 4.655 r_mcangle_it 2.98 r_mcbond_it 2.077 r_angle_refined_deg 1.742 r_nbtor_refined 0.321 r_symmetry_vdw_refined 0.279 r_nbd_refined 0.24 r_chiral_restr 0.161 r_xyhbond_nbd_refined 0.132 r_symmetry_hbond_refined 0.12 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3076 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 35
Software Software Software Name Purpose JDirector data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling