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Crystal structure of bovine lactoperoxidase complexed with cystiene at 1.98A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R4X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 Ammonium Iodide, PEG3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.39 48.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.006 α = 90 b = 80.3 β = 102.02 c = 76.51 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 IMAGE PLATE MARRESEARCH Mirror 2012-11-20 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) 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 1.98 74.83 96.8 43211 40968
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 1.98 2.05 94.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3R4X 1.98 74.83 43211 40968 2181 96.74 0.22412 0.21989 0.2175 0.2353 0.25221 0.2809 RANDOM 40.608
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] -0.68 0.86 -1.6 2.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.485 r_dihedral_angle_3_deg 18.43 r_dihedral_angle_4_deg 17.251 r_dihedral_angle_1_deg 7.493 r_scangle_it 4.157 r_scbond_it 2.988 r_angle_refined_deg 2.065 r_mcangle_it 1.809 r_mcbond_it 1.072 r_chiral_restr 0.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.485 r_dihedral_angle_3_deg 18.43 r_dihedral_angle_4_deg 17.251 r_dihedral_angle_1_deg 7.493 r_scangle_it 4.157 r_scbond_it 2.988 r_angle_refined_deg 2.065 r_mcangle_it 1.809 r_mcbond_it 1.072 r_chiral_restr 0.138 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4774 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 138
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling