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Structure of bovine lactoperoxidase with multiple iodide ions in the distaline heme cavity.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GN6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 Ammonium Iodide, PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP,
Crystal Properties Matthews coefficient Solvent content 2.32 46.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.81 α = 90 b = 80.673 β = 103.07 c = 74.442 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 81 CCD MARRESEARCH 2010-11-10 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) 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 2.42 43.99 93.8 0.114 3.4 4.3 22380
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 2.42 2.48 96 0.314 2.4 6.3
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 4GN6 2.42 43.953 22380 1146 94.053 0.188 0.1836 0.1873 0.2687 0.2614 57.688
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] -0.257 -0.1 -0.025 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.486 r_dihedral_angle_4_deg 17.604 r_dihedral_angle_3_deg 15.525 r_lrange_it 11.264 r_lrange_other 11.257 r_dihedral_angle_1_deg 7.814 r_scangle_it 6.267 r_scangle_other 6.267 r_mcangle_it 6.097 r_mcangle_other 6.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.486 r_dihedral_angle_4_deg 17.604 r_dihedral_angle_3_deg 15.525 r_lrange_it 11.264 r_lrange_other 11.257 r_dihedral_angle_1_deg 7.814 r_scangle_it 6.267 r_scangle_other 6.267 r_mcangle_it 6.097 r_mcangle_other 6.086 r_scbond_it 4.174 r_scbond_other 4.173 r_mcbond_other 4.032 r_mcbond_it 4.031 r_angle_refined_deg 1.474 r_angle_other_deg 1.192 r_nbd_other 0.234 r_symmetry_xyhbond_nbd_refined 0.233 r_xyhbond_nbd_refined 0.231 r_nbd_refined 0.211 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.165 r_symmetry_nbd_refined 0.155 r_metal_ion_refined 0.126 r_symmetry_nbtor_other 0.079 r_chiral_restr_other 0.067 r_chiral_restr 0.063 r_symmetry_xyhbond_nbd_other 0.052 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4771 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 153
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing