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Crystal structure of the complex of lactoperoxidase with nitric oxide at 1.72 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9IT8
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 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.02 α = 90 b = 80.405 β = 103.117 c = 75.844 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) 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 1.72 73.86 99.2 0.06 0.99 7.8 3.5 66501 36
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.75 97.8 1.21 0.65 0.6 3.6
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 1.72 73.86 66439 1320 99.039 0.187 0.1859 0.1957 0.235 0.2444 48.219
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] 0.014 0.019 -0.021 -0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.327 r_dihedral_angle_3_deg 13.844 r_lrange_it 12.589 r_lrange_other 12.588 r_scangle_it 7.643 r_scangle_other 7.642 r_dihedral_angle_1_deg 7.305 r_dihedral_angle_2_deg 7.268 r_mcangle_it 6.848 r_mcangle_other 6.848
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.327 r_dihedral_angle_3_deg 13.844 r_lrange_it 12.589 r_lrange_other 12.588 r_scangle_it 7.643 r_scangle_other 7.642 r_dihedral_angle_1_deg 7.305 r_dihedral_angle_2_deg 7.268 r_mcangle_it 6.848 r_mcangle_other 6.848 r_scbond_it 4.951 r_scbond_other 4.95 r_mcbond_it 4.544 r_mcbond_other 4.505 r_angle_refined_deg 1.727 r_angle_other_deg 1.557 r_metal_ion_refined 0.681 r_nbd_other 0.254 r_symmetry_xyhbond_nbd_refined 0.252 r_nbd_refined 0.242 r_symmetry_nbd_refined 0.217 r_symmetry_nbd_other 0.216 r_xyhbond_nbd_refined 0.21 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_other 0.126 r_symmetry_nbtor_other 0.103 r_chiral_restr 0.082 r_gen_planes_other 0.027 r_gen_planes_refined 0.013 r_bond_refined_d 0.008 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4772 Nucleic Acid Atoms Solvent Atoms 521 Heterogen Atoms 209
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing