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Crystal structure of the complex of goat lactoperoxidase with hypothiocyanite and hydrogen peroxide at 1.79 A resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N7A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 Sodium nitrate, PEG, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.37 48.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.881 α = 90 b = 80.731 β = 101.53 c = 75.139 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 80 CCD MARRESEARCH Mirror 2013-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.79 27.214 96.38 0.099 0.94 7.2 8.3 56910
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.84 84.83 0.89 3.5 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4N7A 1.794 27.214 56910 2871 96.382 0.234 0.231 0.2371 0.2966 0.2981 34.996
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] -0.126 -0.012 0.273 -0.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.919 r_dihedral_angle_4_deg 17.516 r_dihedral_angle_3_deg 16.787 r_lrange_it 8.209 r_lrange_other 8.151 r_dihedral_angle_1_deg 7.982 r_mcangle_it 4.464 r_mcangle_other 4.454 r_scangle_it 4.345 r_scangle_other 4.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.919 r_dihedral_angle_4_deg 17.516 r_dihedral_angle_3_deg 16.787 r_lrange_it 8.209 r_lrange_other 8.151 r_dihedral_angle_1_deg 7.982 r_mcangle_it 4.464 r_mcangle_other 4.454 r_scangle_it 4.345 r_scangle_other 4.344 r_angle_other_deg 3.05 r_chiral_restr_other 2.965 r_mcbond_other 2.903 r_mcbond_it 2.898 r_scbond_it 2.808 r_scbond_other 2.807 r_angle_refined_deg 1.664 r_nbd_other 0.298 r_nbd_refined 0.254 r_symmetry_nbd_other 0.232 r_xyhbond_nbd_refined 0.226 r_symmetry_nbd_refined 0.199 r_symmetry_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.166 r_metal_ion_refined 0.143 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.076 r_symmetry_xyhbond_nbd_other 0.043 r_bond_other_d 0.034 r_gen_planes_other 0.025 r_gen_planes_refined 0.009 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4757 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 175
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing