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Crystal structure of bovine lactoperoxidase with a partial Glu258-heme linkage at 2.07 A resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K1E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 NaNO3, PEG3350, pH6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.13 42.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.012 α = 90 b = 79.809 β = 93.01 c = 66.106 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 2015-11-26 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 2.07 66.01 94.6 0.07 17.3 4.2 32253
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 2.07 2.11 69.1 2.3
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 (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 5K1E 2.07 34.17 31234 1001 94.43 0.16918 0.16711 0.1783 0.23601 0.2373 RANDOM 55.971
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] -2.21 -1.05 -2.33 4.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.337 r_dihedral_angle_4_deg 17.411 r_dihedral_angle_3_deg 16.864 r_long_range_B_refined 8.402 r_long_range_B_other 8.402 r_dihedral_angle_1_deg 8.29 r_mcangle_it 3.398 r_mcangle_other 3.393 r_scangle_other 3.108 r_angle_refined_deg 2.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.337 r_dihedral_angle_4_deg 17.411 r_dihedral_angle_3_deg 16.864 r_long_range_B_refined 8.402 r_long_range_B_other 8.402 r_dihedral_angle_1_deg 8.29 r_mcangle_it 3.398 r_mcangle_other 3.393 r_scangle_other 3.108 r_angle_refined_deg 2.298 r_mcbond_other 2.073 r_mcbond_it 2.072 r_scbond_it 2.001 r_scbond_other 1.998 r_angle_other_deg 1.261 r_chiral_restr 0.141 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_gen_planes_other 0.006 r_bond_other_d 0.002 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 269 Heterogen Atoms 170
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing