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Crystal structure of the complex of buffalo Lactoperoxidase with fluoride ion at 3.5A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O86 PDB entry 2O86
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 290 TRIS-HCL, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.44 49.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.127 α = 90 b = 80.739 β = 102.94 c = 77.699 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 290 IMAGE PLATE MARRESEARCH Mirror 2007-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54
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 3.5 75.81 83.6 0.129 3.9 3.1 6641 64.2
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 3.5 3.62 87.7 0.184 1.9 3.1 6641
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 PDB entry 2O86 3.5 75.81 6641 324 83.19 0.22182 0.22117 0.2107 0.23484 0.2245 RANDOM 27.023
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] -0.71 -0.93 -4.6 4.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.636 r_dihedral_angle_3_deg 18.978 r_dihedral_angle_4_deg 15.72 r_dihedral_angle_1_deg 2.376 r_angle_refined_deg 1.991 r_symmetry_hbond_refined 0.331 r_nbtor_refined 0.327 r_symmetry_vdw_refined 0.286 r_nbd_refined 0.247 r_xyhbond_nbd_refined 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.636 r_dihedral_angle_3_deg 18.978 r_dihedral_angle_4_deg 15.72 r_dihedral_angle_1_deg 2.376 r_angle_refined_deg 1.991 r_symmetry_hbond_refined 0.331 r_nbtor_refined 0.327 r_symmetry_vdw_refined 0.286 r_nbd_refined 0.247 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.131 r_metal_ion_refined 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_mcbond_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4770 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 194
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection AUTOMAR data reduction SCALEPACK data scaling AMoRE phasing