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Structure of native leukocyte myeloperoxidase in complex with a truncated version of the Staphylococcal Peroxidase Inhibitor SPIN and iodide at pH 5.5
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 5.5 295.15 0.1 M Na Acet 5.5 pH
6 %(w/v) PEG 8K
10 %(w/v) PEG 1K
0.4 M NaI
Crystal Properties Matthews coefficient Solvent content 2.33 47.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.361 α = 90 b = 111.361 β = 90 c = 242.068 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 16M Toroidal mirror 2023-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.9075 ESRF ID23-1
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 2.63 101.17 93.8 0.343 0.359 0.105 0.931 6.9 11.5 38848
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 2.63 2.81 55.7 2.538 2.657 0.782 0.578 1.4
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 (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 2.63 101.17 36923 1925 84.68 0.19498 0.19217 0.199 0.2494 0.2546 RANDOM 48.555
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] -0.58 -0.58 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.689 r_dihedral_angle_2_deg 12.802 r_long_range_B_refined 6.738 r_long_range_B_other 6.732 r_dihedral_angle_1_deg 6.588 r_scangle_other 4.363 r_mcangle_it 3.364 r_mcangle_other 3.363 r_scbond_it 2.705 r_scbond_other 2.705
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.689 r_dihedral_angle_2_deg 12.802 r_long_range_B_refined 6.738 r_long_range_B_other 6.732 r_dihedral_angle_1_deg 6.588 r_scangle_other 4.363 r_mcangle_it 3.364 r_mcangle_other 3.363 r_scbond_it 2.705 r_scbond_other 2.705 r_mcbond_it 2.086 r_mcbond_other 2.086 r_angle_refined_deg 1.809 r_angle_other_deg 0.603 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 10077 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 434
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing