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Structure of native leukocyte myeloperoxidase in complex with a truncated version of the Staphylococcal Peroxidase Inhibitor SPIN and thiocyanate 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 (Buffer)
4 %(w/v) PEG 8K (Precipitant)
10 %(w/v) PEG 1K (Precipitant)
0.4 M KSCN (Salt)
Crystal Properties Matthews coefficient Solvent content 2.33 47.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.328 α = 90 b = 111.328 β = 90 c = 242.725 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 0.8856 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 1.9 101.192 93.3 0.256 0.272 0.09 0.977 6.7 9.1 86444
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 1.9 2.101 66.4 3.456 3.729 1.372 0.241 1.7 7.7
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 1.903 101.192 86440 4245 72.106 0.171 0.1682 0.1683 0.2158 0.216 RANDOM 38.466
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] -0.128 -0.128 0.255
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.759 r_dihedral_angle_3_deg 14.04 r_dihedral_angle_2_deg 13.065 r_dihedral_angle_1_deg 6.865 r_lrange_it 6.4 r_lrange_other 6.351 r_scangle_it 4.725 r_scangle_other 4.724 r_scbond_it 3.196 r_scbond_other 3.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.759 r_dihedral_angle_3_deg 14.04 r_dihedral_angle_2_deg 13.065 r_dihedral_angle_1_deg 6.865 r_lrange_it 6.4 r_lrange_other 6.351 r_scangle_it 4.725 r_scangle_other 4.724 r_scbond_it 3.196 r_scbond_other 3.196 r_mcangle_it 2.96 r_mcangle_other 2.96 r_mcbond_it 2.104 r_mcbond_other 2.104 r_angle_refined_deg 2.009 r_dihedral_angle_other_2_deg 0.779 r_angle_other_deg 0.66 r_symmetry_xyhbond_nbd_refined 0.542 r_nbd_refined 0.255 r_symmetry_nbd_refined 0.243 r_symmetry_nbd_other 0.191 r_nbd_other 0.19 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.168 r_ncsr_local_group_2 0.147 r_symmetry_xyhbond_nbd_other 0.132 r_ncsr_local_group_3 0.107 r_chiral_restr 0.092 r_metal_ion_refined 0.088 r_symmetry_nbtor_other 0.085 r_ncsr_local_group_1 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10063 Nucleic Acid Atoms Solvent Atoms 775 Heterogen Atoms 373
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing