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Crystal structure of ternary complexes of lactoperoxidase with hydrogen peroxide at 1.70 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QL6
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 2.4 48.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.92 α = 90 b = 79.498 β = 102.25 c = 77.723 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 1.7 75.9 96 0.068 11 9.2 67857
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 1.7 1.74 96.2 0.33 5.2
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 3ql6 1.7 26.707 66994 3384 94.999 0.183 0.1814 0.1908 0.2043 0.2142 29.047
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] 0.018 0.014 -0.046 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.542 r_dihedral_angle_4_deg 15.009 r_dihedral_angle_3_deg 13.885 r_lrange_other 10.287 r_lrange_it 10.286 r_dihedral_angle_1_deg 7.261 r_scangle_it 5.288 r_scangle_other 5.287 r_mcangle_it 5.049 r_mcangle_other 5.042
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.542 r_dihedral_angle_4_deg 15.009 r_dihedral_angle_3_deg 13.885 r_lrange_other 10.287 r_lrange_it 10.286 r_dihedral_angle_1_deg 7.261 r_scangle_it 5.288 r_scangle_other 5.287 r_mcangle_it 5.049 r_mcangle_other 5.042 r_scbond_it 3.408 r_scbond_other 3.407 r_mcbond_it 3.159 r_mcbond_other 3.134 r_chiral_restr_other 2.966 r_angle_other_deg 2.561 r_angle_refined_deg 1.827 r_symmetry_nbd_refined 0.307 r_nbd_other 0.244 r_nbd_refined 0.22 r_symmetry_nbd_other 0.218 r_xyhbond_nbd_refined 0.211 r_symmetry_xyhbond_nbd_refined 0.193 r_nbtor_refined 0.174 r_symmetry_xyhbond_nbd_other 0.14 r_xyhbond_nbd_other 0.135 r_chiral_restr 0.097 r_metal_ion_refined 0.097 r_symmetry_nbtor_other 0.078 r_bond_other_d 0.034 r_symmetry_metal_ion_refined 0.034 r_gen_planes_other 0.02 r_bond_refined_d 0.012 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4770 Nucleic Acid Atoms Solvent Atoms 659 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing