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Crystal structure of the complex of bovine lactoperoxidase with salicylhydroxamic acid at 2.34 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PT3 PDB ENTRY 2PT3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 298 Tris-HCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.46 50.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.618 α = 90 b = 80.553 β = 102.56 c = 77.803 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 291 IMAGE PLATE MAR scanner 345 mm plate Mirror 2007-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54172
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 2.34 20 98.5 27454 26567
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 2.34 2.41 95.2
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 PDB ENTRY 2PT3 2.34 20 27454 26567 871 98.53 0.201 0.17382 0.17235 0.176 0.21952 0.2199 RANDOM 36.966
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] -0.11 -0.28 -1.7 1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.327 r_scangle_it 4.38 r_dihedral_angle_1_deg 3.051 r_scbond_it 2.767 r_mcangle_it 2.005 r_angle_refined_deg 1.718 r_mcbond_it 1.073 r_symmetry_hbond_refined 0.276 r_nbd_refined 0.254 r_symmetry_vdw_refined 0.181
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.327 r_scangle_it 4.38 r_dihedral_angle_1_deg 3.051 r_scbond_it 2.767 r_mcangle_it 2.005 r_angle_refined_deg 1.718 r_mcbond_it 1.073 r_symmetry_hbond_refined 0.276 r_nbd_refined 0.254 r_symmetry_vdw_refined 0.181 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.115 r_metal_ion_refined 0.083 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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 4774 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 200
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing