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Structure of bovine Lactoperoxidase with a partially modified covalent bond with heme moiety
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4S0Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 Ammonium Iodide, PEG, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.005 α = 90 b = 79.834 β = 102.3 c = 76.126 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 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 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 1.93 50 100 0.08 24.2 4.6 47548 26.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 1.96 100 2.2 4.4
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 4S0Y 1.93 50 45122 2406 99.96 0.19459 0.19181 0.2038 0.24548 0.2522 RANDOM 40.953
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] -0.13 -0.47 -2.38 2.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.819 r_dihedral_angle_4_deg 16.672 r_dihedral_angle_3_deg 15.933 r_long_range_B_refined 8.944 r_long_range_B_other 8.944 r_dihedral_angle_1_deg 7.966 r_mcangle_it 6.091 r_mcangle_other 6.085 r_scangle_other 5.996 r_mcbond_it 4.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.819 r_dihedral_angle_4_deg 16.672 r_dihedral_angle_3_deg 15.933 r_long_range_B_refined 8.944 r_long_range_B_other 8.944 r_dihedral_angle_1_deg 7.966 r_mcangle_it 6.091 r_mcangle_other 6.085 r_scangle_other 5.996 r_mcbond_it 4.075 r_mcbond_other 4.057 r_scbond_it 3.945 r_scbond_other 3.945 r_angle_refined_deg 2.092 r_angle_other_deg 1.158 r_chiral_restr 0.129 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_gen_planes_other 0.006 r_bond_other_d 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4771 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 149
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing