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Staphylococcus aureus endonuclease IV Y33F mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8AXY 8AXY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 Protein in 20 mM phosphate. Precipitant: 20-30% polyethylene glycol 3350, 200 mM NaCl, 100 mM BisTris, pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.91 35.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.477 α = 90 b = 41.987 β = 90 c = 152.773 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 150 PIXEL DECTRIS EIGER2 XE 16M mirrors 2022-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.47 152.77 100 0.181 0.189 0.052 0.998 7.3 13.19 41699 19.04
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.5 99.86 3.394 3.527 0.955 0.305 0.4 13.51
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 8AXY 1.5 40.49 1.34 41667 3813 99.53 0.1721 0.1704 0.1711 0.2038 0.2045 25.64
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 5.7534 f_angle_d 0.7555 f_chiral_restr 0.0491 f_plane_restr 0.0067 f_bond_d 0.0054
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2332 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement DIALS data reduction xia2 data scaling PHASER phasing