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Structure of native leukocyte myeloperoxidase in complex with a truncated version (SPIN truncated) of the Staphyloccal Peroxidase Inhibitor SPIN from Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QZR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 8% (w/V) PEG 20000, 0.1 M BICINE pH 9, 0.5% (V/V) Dioxane
Crystal Properties Matthews coefficient Solvent content 2.94 58.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 257.022 α = 90 b = 157.196 β = 90 c = 166.56 γ = 90
Symmetry Space Group P 21 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 PIXEL DECTRIS PILATUS3 2M 2021-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.26 76.19 99.92 0.3967 0.969 3.64 7.5 315034 32.82
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.26 2.341 0.173
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 7QZR 2.28 76.19 1.34 242588 12022 79.23 0.1768 0.1741 0.1751 0.2291 0.2281 40.3
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 15.6979 f_angle_d 1.3225 f_chiral_restr 0.0564 f_bond_d 0.0136 f_plane_restr 0.0117
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 40206 Nucleic Acid Atoms Solvent Atoms 1068 Heterogen Atoms 1522
Software Software Software Name Purpose autoPROC data processing XDS data reduction Aimless data scaling STARANISO data scaling MoRDa phasing Coot model building PHENIX refinement