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Crystal structure of Deoxyuridine 5'-triphosphate nucleotidohydrolase from Legionella pneumophila Philadelphia 1 in complex with dUMP (Deoxyuridine 5'-monophosphate)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MAI apo structure, 6MAI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 285 Molecular Dimensions Morpheus screen, condition C4: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 30mM each sodium nitrate, disodium hydrogen phosphate, ammonium sulfate: 100mM MES/imidazole pH 6.5: LepnA.01206.a.B1.PS38438 at 24.33mg/ml: 2h soak with 5mM MgCl2 + dUTP with was converted to dUMP: cryo: direct: EG in two steps: tray 301633a1, puck PXP9-8
Crystal Properties Matthews coefficient Solvent content 3.38 63.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.67 α = 90 b = 85.67 β = 90 c = 55.46 γ = 120
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 RIGAKU SATURN 944+ 2018-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 37.096 100 0.059 0.063 0.999 22.98 9.282 17033 34.444
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 99.9 0.47 0.523 0.878 3.04 5.22
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT apo structure, 6MAI 1.95 37.096 1.35 17031 1774 99.97 0.1515 0.1482 0.1811 0.1777 34.5277
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.83 f_angle_d 0.933 f_chiral_restr 0.074 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1044 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 33
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing Coot model building