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The 3D structure of D95N mutant DUTPase from phage phi11 of S. aureus reveals the molecular details for the coordination of a structural Mg(II) ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GV8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.6 293 0.1M sodium acetate, 15 - 41.5% MPD, 0.02M calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.28 46.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.42 α = 90 b = 108.42 β = 90 c = 167.05 γ = 90
Symmetry Space Group P 43 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 IMAGE PLATE RIGAKU RAXIS IV++ 2014-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.25 19.57 100 0.208 8.6 9.1 22585
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 2.9 3 99.9 0.358
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 FREE R-VALUE 4GV8 2.9 19.57 1.34 22581 1136 99.51 0.211 0.2085 0.2159 0.2583 0.2618 42.1
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 11.718 f_angle_d 0.932 f_chiral_restr 0.038 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6883 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 174
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing