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Crystal structure of the complex of lactoperoxidase with bromo methane at 2.41 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OGW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.26 45.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.742 α = 90 b = 80.379 β = 103.5 c = 73.177 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 77 CCD MARRESEARCH mirror 2013-11-26 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 2.41 71.16 99.3 0.129 16.5 23328 23328
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 2.41 2.47 92.3 0.379 2.2
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 (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 3OGW 2.41 71.15 21994 1190 98.96 0.22302 0.21869 0.2253 0.2991 0.293 RANDOM 38.347
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] -0.4 -2.66 -2.53 1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.054 r_dihedral_angle_3_deg 17.214 r_dihedral_angle_4_deg 14.439 r_dihedral_angle_1_deg 7.105 r_scbond_it 2.042 r_angle_refined_deg 1.619 r_mcangle_it 1.46 r_mcbond_it 0.785 r_chiral_restr 0.109 r_bond_refined_d 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.054 r_dihedral_angle_3_deg 17.214 r_dihedral_angle_4_deg 14.439 r_dihedral_angle_1_deg 7.105 r_scbond_it 2.042 r_angle_refined_deg 1.619 r_mcangle_it 1.46 r_mcbond_it 0.785 r_chiral_restr 0.109 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4774 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement