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Staphylococcus aureus endonuclease IV with bound phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8AXY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 200 nl protein mixed with 200 nl precipitant
Protein: 9 mg/ml in 20 mM Tris-HCl pH 8.0, 150 mM NaCl was mixed with 20 mM phosphate (final concentration).
Precipitant: 28% PEG 3350, 250 mM NaCl, 100 mM Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.51 51.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.548 α = 90 b = 84.04 β = 90 c = 103.344 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2023-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.87313 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.9 44 99.82 0.2088 0.229 0.09284 0.991 9.7 5.9 50721 30.48
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.98 100 1.165 2.278 1.5 6.14
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.9 44 1.93 50721 2586 99.23 0.1888 0.1877 0.1874 0.2112 0.2102 33.89
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 5.4943 f_angle_d 0.7595 f_chiral_restr 0.0496 f_plane_restr 0.0069 f_bond_d 0.0064
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2333 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 10
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing