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Structure of native leukocyte myeloperoxidase in complex with a truncated version of the Staphylococcal Peroxidase Inhibitor SPIN and bromide at pH 7.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7Z53
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295.15 0.1 M TRIS 7.5 pH
6 %(w/v) PEG 8K
8 %(w/v) PEG 1K
0.4 M NaI
Crystal Properties Matthews coefficient Solvent content 2.59 52.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.919 α = 90 b = 111.919 β = 90 c = 241.758 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 213.15 PIXEL DECTRIS EIGER X 9M Vertical CRL / Horizontal Eliptical mirror 2023-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 1.9075 ESRF ID30B
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 2.21 49.01 94 0.324 0.329 0.056 0.992 17.5 35.8 66495
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 2.21 2.35 51.5 2.367 2.423 0.498 0.544 1.5 21.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.21 48.08 63168 3326 86.15 0.19546 0.19251 0.25234 0.2507 RANDOM 20.829
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] -0.15 -0.15 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.171 r_dihedral_angle_2_deg 11.115 r_dihedral_angle_1_deg 7.077 r_long_range_B_refined 3.228 r_long_range_B_other 2.597 r_angle_refined_deg 1.603 r_angle_other_deg 0.547 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.171 r_dihedral_angle_2_deg 11.115 r_dihedral_angle_1_deg 7.077 r_long_range_B_refined 3.228 r_long_range_B_other 2.597 r_angle_refined_deg 1.603 r_angle_other_deg 0.547 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10077 Nucleic Acid Atoms Solvent Atoms 738 Heterogen Atoms 324
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing