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Crystal structure of bovine lactoperoxidase with partial occupancies of iodide and SCN- ions at the substrate binding site on the distal heme side at 1.92 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YD9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 0.2M AMMONIUM IODIDE, 20% PEG3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, 298K.
Crystal Properties Matthews coefficient Solvent content 2.06 40.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.74 α = 90 b = 79.8 β = 91.43 c = 65.18 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 CCD MARRESEARCH mirror 2017-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.92 65.17 96.4 0.041 12.3 2.8 40370
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.95 98.4 0.46 2 2.8
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 (Observed) 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 5yd9 1.92 50.52 38471 1899 95.25 0.2249 0.22207 0.2268 0.27909 0.2797 RANDOM 56.397
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] -3.01 -1.47 -1.3 4.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.397 r_dihedral_angle_4_deg 18.855 r_dihedral_angle_3_deg 18.369 r_long_range_B_refined 10.245 r_long_range_B_other 10.245 r_dihedral_angle_1_deg 8.383 r_mcangle_it 6.883 r_mcangle_other 6.882 r_scangle_other 6.596 r_mcbond_it 4.769
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.397 r_dihedral_angle_4_deg 18.855 r_dihedral_angle_3_deg 18.369 r_long_range_B_refined 10.245 r_long_range_B_other 10.245 r_dihedral_angle_1_deg 8.383 r_mcangle_it 6.883 r_mcangle_other 6.882 r_scangle_other 6.596 r_mcbond_it 4.769 r_mcbond_other 4.755 r_scbond_it 4.482 r_scbond_other 4.48 r_angle_refined_deg 1.644 r_angle_other_deg 0.867 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4774 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling MOLREP phasing