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Crystal structure of the ternary complex of lactoperoxidase with nitric oxide and nitrite ion at 1.95 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8ING
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 0.2M AMMONIUM IODIDE, 21% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.38 48.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.048 α = 90 b = 80.503 β = 102.849 c = 75.951 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 X 9M 2023-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.87 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.95 74.05 99.6 0.068 0.094 0.973 7.2 3.4 45886
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 95.2 0.763 0.725 0.658 0.9 3.5
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.954 74.049 45840 1357 99.496 0.19 0.1884 0.1979 0.2474 0.2519 53.701
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] -1.108 1.371 -2.794 2.968
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.372 r_dihedral_angle_3_deg 14.311 r_lrange_it 12.545 r_lrange_other 12.544 r_dihedral_angle_1_deg 7.355 r_scangle_it 7.282 r_scangle_other 7.281 r_mcangle_it 7.168 r_mcangle_other 7.167 r_dihedral_angle_2_deg 5.969
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.372 r_dihedral_angle_3_deg 14.311 r_lrange_it 12.545 r_lrange_other 12.544 r_dihedral_angle_1_deg 7.355 r_scangle_it 7.282 r_scangle_other 7.281 r_mcangle_it 7.168 r_mcangle_other 7.167 r_dihedral_angle_2_deg 5.969 r_mcbond_it 4.715 r_mcbond_other 4.694 r_scbond_it 4.614 r_scbond_other 4.613 r_chiral_restr_other 2.966 r_angle_refined_deg 1.727 r_angle_other_deg 1.508 r_nbd_other 0.238 r_nbd_refined 0.224 r_symmetry_nbd_other 0.216 r_symmetry_nbd_refined 0.215 r_xyhbond_nbd_refined 0.207 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.149 r_symmetry_nbtor_other 0.098 r_symmetry_xyhbond_nbd_other 0.091 r_chiral_restr 0.086 r_gen_planes_other 0.026 r_gen_planes_refined 0.012 r_bond_refined_d 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4771 Nucleic Acid Atoms Solvent Atoms 338 Heterogen Atoms 199
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing