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Structure of native leukocyte myeloperoxidase in complex with a truncated version of the Staphylococcal Peroxidase Inhibitor SPIN and selenocyanate 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 (Buffer)
6 %(w/v) PEG 8K (Precipitant)
10 %(w/v) PEG 1K (Precipitant)
0.4 M KSeCN (Salt)
Crystal Properties Matthews coefficient Solvent content 2.31 46.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.507 α = 90 b = 110.507 β = 90 c = 241.574 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 2.058 19.89 94.3 0.353 0.386 0.1 0.993 2.3576 13.4 62476
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 2.058 2.303 65.2 3.255 3.384 0.92 0.54 1.6 13.4
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 2.06 19.89 62471 3150 68.404 0.182 0.1788 0.1795 0.2342 0.2379 RANDOM 39.025
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] -0.008 -0.008 0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.041 r_dihedral_angle_3_deg 14.631 r_dihedral_angle_2_deg 11.644 r_dihedral_angle_1_deg 7.47 r_lrange_it 5.698 r_lrange_other 5.693 r_scangle_it 4.146 r_scangle_other 4.145 r_mcangle_it 3.371 r_mcangle_other 3.371
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.041 r_dihedral_angle_3_deg 14.631 r_dihedral_angle_2_deg 11.644 r_dihedral_angle_1_deg 7.47 r_lrange_it 5.698 r_lrange_other 5.693 r_scangle_it 4.146 r_scangle_other 4.145 r_mcangle_it 3.371 r_mcangle_other 3.371 r_scbond_it 2.68 r_scbond_other 2.68 r_mcbond_it 2.2 r_mcbond_other 2.192 r_angle_refined_deg 1.904 r_dihedral_angle_other_2_deg 1.486 r_angle_other_deg 0.738 r_nbd_refined 0.195 r_nbtor_refined 0.165 r_symmetry_xyhbond_nbd_refined 0.156 r_symmetry_nbd_other 0.155 r_xyhbond_nbd_refined 0.136 r_symmetry_nbd_refined 0.133 r_ncsr_local_group_1 0.113 r_nbd_other 0.103 r_ncsr_local_group_2 0.096 r_chiral_restr 0.093 r_ncsr_local_group_3 0.08 r_symmetry_nbtor_other 0.073 r_symmetry_xyhbond_nbd_other 0.059 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10063 Nucleic Acid Atoms Solvent Atoms 403 Heterogen Atoms 360
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling XDS data scaling MOLREP phasing