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Crystal Structure of bovine lactoperoxidase with iodide ions at 2.9A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IPS
Crystallization Crystal Properties Matthews coefficient Solvent content 2.45 49.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.53 α = 90 b = 80.549 β = 103.74 c = 78.031 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 MAR scanner 345 mm plate mirror 2006-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 2.9 25 98.6 0.17 6.5 13026 13026 38.9
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 2.9 3 97.1 0.406 2.1
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2IPS 2.95 25 13026 13026 681 98.5 0.198 0.19603 0.2363 RANDOM 25.324
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] 0.1 -0.91 -0.73 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.057 r_dihedral_angle_3_deg 16.57 r_dihedral_angle_4_deg 14.941 r_dihedral_angle_1_deg 4.233 r_mcangle_it 3.046 r_mcbond_it 2.122 r_scangle_it 1.726 r_angle_refined_deg 1.212 r_scbond_it 1.024 r_symmetry_hbond_refined 0.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.057 r_dihedral_angle_3_deg 16.57 r_dihedral_angle_4_deg 14.941 r_dihedral_angle_1_deg 4.233 r_mcangle_it 3.046 r_mcbond_it 2.122 r_scangle_it 1.726 r_angle_refined_deg 1.212 r_scbond_it 1.024 r_symmetry_hbond_refined 0.412 r_nbtor_refined 0.314 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.141 r_symmetry_vdw_refined 0.112 r_chiral_restr 0.091 r_metal_ion_refined 0.083 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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 4770 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 193
Software Software Software Name Purpose REFMAC refinement MAR345 data collection AUTOMAR data reduction SCALEPACK data scaling AMoRE phasing