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Crystal structure of Buffalo lactoperoxidase with Rhodanide at 2.09 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O86
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 Ammonium Iodide
Crystal Properties Matthews coefficient Solvent content 2.39 48.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.012 α = 90 b = 80.047 β = 102.64 c = 76.8 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 2014-11-15 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 Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.09 50 98.6 0.133 0.154 0.077 12 3.9 37445
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.13 100 0.773 0.89 0.438 0.781 4.1 1849
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 2O86 2.1 35.33 34643 1821 97.38 0.2387 0.2356 0.2515 0.2981 0.3073 RANDOM 52.09
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] -0.79 -1.19 -1.61 2.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.82 r_dihedral_angle_3_deg 18.647 r_dihedral_angle_4_deg 17.581 r_dihedral_angle_1_deg 7.934 r_mcangle_it 5.89 r_mcbond_it 4.131 r_mcbond_other 4.119 r_angle_refined_deg 1.823 r_angle_other_deg 0.91 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.82 r_dihedral_angle_3_deg 18.647 r_dihedral_angle_4_deg 17.581 r_dihedral_angle_1_deg 7.934 r_mcangle_it 5.89 r_mcbond_it 4.131 r_mcbond_other 4.119 r_angle_refined_deg 1.823 r_angle_other_deg 0.91 r_chiral_restr 0.112 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4770 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection PDB_EXTRACT data extraction AUTOMAR data reduction AUTOMAR data scaling AMoRE phasing