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Crystal structure of bovine lactoperoxidase with hydrogen peroxide trapped between heme iron and his109 at 1.69 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q9K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 0.2M Ammonium Iodide, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.38 48.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.913 α = 90 b = 79.69 β = 102.23 c = 76.965 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 2010-10-21 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) 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 1.696 39.41 99.3 0.079 12 8.2 70470
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 1.696 1.74 93.9 0.59
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 3q9k 1.696 39.41 68757 3464 97.577 0.199 0.1974 0.2044 0.2346 0.238 36.084
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] 0.008 0.033 -0.018 -0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.766 r_dihedral_angle_4_deg 14.896 r_dihedral_angle_3_deg 14.349 r_lrange_it 9.119 r_lrange_other 9.119 r_dihedral_angle_1_deg 7.19 r_scangle_it 5.312 r_scangle_other 5.311 r_mcangle_it 5.167 r_mcangle_other 5.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.766 r_dihedral_angle_4_deg 14.896 r_dihedral_angle_3_deg 14.349 r_lrange_it 9.119 r_lrange_other 9.119 r_dihedral_angle_1_deg 7.19 r_scangle_it 5.312 r_scangle_other 5.311 r_mcangle_it 5.167 r_mcangle_other 5.163 r_scbond_it 3.504 r_scbond_other 3.503 r_mcbond_it 3.357 r_mcbond_other 3.346 r_chiral_restr_other 2.965 r_angle_other_deg 2.587 r_angle_refined_deg 1.75 r_nbd_other 0.254 r_symmetry_nbd_other 0.221 r_xyhbond_nbd_refined 0.22 r_nbd_refined 0.216 r_symmetry_nbd_refined 0.216 r_symmetry_xyhbond_nbd_refined 0.192 r_symmetry_xyhbond_nbd_other 0.178 r_nbtor_refined 0.173 r_metal_ion_refined 0.108 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.079 r_bond_other_d 0.034 r_gen_planes_other 0.016 r_bond_refined_d 0.011 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4770 Nucleic Acid Atoms Solvent Atoms 654 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing