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Structure of monomerized native leukocyte myeloperoxidase in complex with the Staphylococcal Peroxidase Inhibitor SPIN
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 7.5 293.15 0.1 M TRIS 7.5 pH,
8 %w/v PEG 1K,
8 %w/v PEG 8K,
0.4 M KSCN
Crystal Properties Matthews coefficient Solvent content 2.52 51.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.474 α = 90 b = 111.474 β = 90 c = 241.912 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 4M 2023-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
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 2.55 78.95 95 0.21 0.219 0.062 0.995 8.4 12.4 30405
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 2.55 2.88 73.5 1.468 1.532 0.433 0.714 1.6 12.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.55 78.95 28896 1509 60.25 0.20485 0.2017 0.2027 0.26438 0.2641 RANDOM 61.293
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] -0.71 -0.71 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.74 r_dihedral_angle_2_deg 10.321 r_dihedral_angle_1_deg 7.231 r_long_range_B_refined 6.333 r_long_range_B_other 6.333 r_scangle_other 3.463 r_mcangle_it 2.878 r_mcangle_other 2.877 r_scbond_it 2.163 r_scbond_other 2.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.74 r_dihedral_angle_2_deg 10.321 r_dihedral_angle_1_deg 7.231 r_long_range_B_refined 6.333 r_long_range_B_other 6.333 r_scangle_other 3.463 r_mcangle_it 2.878 r_mcangle_other 2.877 r_scbond_it 2.163 r_scbond_other 2.163 r_mcbond_it 1.686 r_mcbond_other 1.686 r_angle_refined_deg 1.479 r_angle_other_deg 0.496 r_chiral_restr 0.064 r_bond_refined_d 0.006 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10150 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 369
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing PDB_EXTRACT data extraction