☰ Navigation Tabs
Structure of monomerized and de-glycosylated 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 293.15 0.2M MgCl2
20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.06 40.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.819 α = 90 b = 84.075 β = 90 c = 128.637 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 213 PIXEL DECTRIS EIGER2 S 9M ELLIPTICAL 2025-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87 ESRF ID23-2
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 1.437 70.377 93.4 0.275 0.291 0.094 0.992 7.4 9.5 87698
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 1.437 1.572 49.7 2.519 2.65 0.813 0.277 1.5 10.4
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 (All) 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 1.44 70.377 87696 4408 78.233 0.143 0.1398 0.14 0.1963 0.1967 RANDOM 14.507
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] 0.639 -0.751 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.86 r_lrange_it 13.854 r_lrange_other 13.236 r_dihedral_angle_3_deg 12.357 r_dihedral_angle_2_deg 12.231 r_scangle_it 10.589 r_scangle_other 10.587 r_mcangle_other 7.573 r_mcangle_it 7.571 r_scbond_it 7.509
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.86 r_lrange_it 13.854 r_lrange_other 13.236 r_dihedral_angle_3_deg 12.357 r_dihedral_angle_2_deg 12.231 r_scangle_it 10.589 r_scangle_other 10.587 r_mcangle_other 7.573 r_mcangle_it 7.571 r_scbond_it 7.509 r_scbond_other 7.5 r_dihedral_angle_1_deg 6.555 r_mcbond_it 5.143 r_mcbond_other 5.14 r_rigid_bond_restr 4.272 r_angle_refined_deg 1.968 r_angle_other_deg 0.683 r_dihedral_angle_other_2_deg 0.533 r_nbd_refined 0.23 r_nbd_other 0.202 r_xyhbond_nbd_refined 0.201 r_symmetry_nbd_refined 0.198 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.174 r_symmetry_xyhbond_nbd_refined 0.159 r_chiral_restr 0.1 r_symmetry_xyhbond_nbd_other 0.092 r_symmetry_nbtor_other 0.079 r_metal_ion_refined 0.064 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5061 Nucleic Acid Atoms Solvent Atoms 520 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement Aimless data scaling gemmi data extraction XDS data reduction MOLREP phasing PDB_EXTRACT data extraction