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Crystal Structure of dUTP pyrophosphatase protein, from Naegleria fowleri in complex with deoxyuridine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OOP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 290 JCSG+ C6: 40% PEG 300 + 100mM Sodium phosphate dibasic / sodium citrate pH 4.2:cryo:direct. PW37974 22.5mg/mL, 0.4+0.4, 6 mM dUTP + 6 mM MgCl2 puck xbp1-8, tray286723C6
Crystal Properties Matthews coefficient Solvent content 2.02 39.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.23 α = 90 b = 74.23 β = 90 c = 74.23 γ = 90
Symmetry Space Group P 21 3
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 RAYONIX MX-300 Beryllium Lenses 2017-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97856 APS 21-ID-F
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 1.45 33.197 100 0.039 0.041 1 46.35 16.992 24498 21.781
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 1.45 1.49 100 0.497 0.512 0.959 5.79 16.977
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4OOP 1.45 33.197 1.35 24472 2039 99.98 0.1369 0.1339 0.1358 0.1698 0.1707
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 14.627 f_angle_d 0.783 f_chiral_restr 0.081 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1082 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 27
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing