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Crystal structure of the complex of lactoperoxidase with four inorganic substrates, SCN, I, Br and Cl
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8K5M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 298 0.2 M Ammonium iodide, 20%(w/v) PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298 K
Crystal Properties Matthews coefficient Solvent content 2.25 45.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.35 α = 90 b = 80.332 β = 103.94 c = 73.391 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 298 CCD MARMOSAIC 325 mm CCD 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 1.99 43.521 96.7 0.082 29.8 6.2 39294
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 1.99 2.05 77 0.31 4.3
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 8K5M 2 43.521 39294 1971 96.496 0.153 0.1506 0.1602 0.1951 0.2009 29.645
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] -0.035 -0.01 0.055 -0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.321 r_dihedral_angle_3_deg 13.041 r_lrange_it 9.892 r_lrange_other 9.869 r_dihedral_angle_1_deg 6.873 r_dihedral_angle_2_deg 6.812 r_scangle_it 5.743 r_scangle_other 5.743 r_mcangle_other 5.335 r_mcangle_it 5.334
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.321 r_dihedral_angle_3_deg 13.041 r_lrange_it 9.892 r_lrange_other 9.869 r_dihedral_angle_1_deg 6.873 r_dihedral_angle_2_deg 6.812 r_scangle_it 5.743 r_scangle_other 5.743 r_mcangle_other 5.335 r_mcangle_it 5.334 r_scbond_it 3.463 r_scbond_other 3.463 r_mcbond_it 3.283 r_mcbond_other 3.273 r_angle_refined_deg 1.684 r_angle_other_deg 0.783 r_symmetry_nbd_refined 0.347 r_nbd_other 0.313 r_nbd_refined 0.227 r_symmetry_nbd_other 0.213 r_symmetry_xyhbond_nbd_refined 0.207 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.181 r_symmetry_nbtor_other 0.111 r_chiral_restr 0.085 r_symmetry_xyhbond_nbd_other 0.047 r_bond_other_d 0.013 r_gen_planes_other 0.011 r_gen_planes_refined 0.01 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4742 Nucleic Acid Atoms Solvent Atoms 407 Heterogen Atoms 205
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building