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The crystal structure of thymidylate kinase from Pseudomonas aeruginosa PAO1 in complex with deoxythymidine.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E5U PDB ENTRY 4E5U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 0.8M Lithium Chloride,
0.1M Tris:HCl,
32% (w/v) PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.17 43.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.352 α = 90 b = 55.352 β = 90 c = 114.767 γ = 120
Symmetry Space Group P 32 2 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 ADSC QUANTUM 315 mirror 2012-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97931 APS 19-ID
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 1.95 37 99.5 0.063 38.4 7 15472 15472
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.98 100 0.687 2.9 7.3 766
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB ENTRY 4E5U 1.95 36.789 1.34 15434 15434 773 99.5 0.1838 0.1838 0.1816 0.1808 0.2257 0.2176 Random
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] 2.672 2.672 -5.3441
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.958 f_angle_d 0.996 f_chiral_restr 0.065 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1604 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 17
Software Software Software Name Purpose SBC-Collect data collection MOLREP phasing PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling