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Crystal structure of the complex of bovine lactoperoxidase with mercaptoimidazole at 2.3 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BXI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 280 Tris hydrochloride, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.63 α = 90 b = 80.667 β = 102.6 c = 77.68 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 MARRESEARCH MIRROR 2006-02-13 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 2.3 20 99.4 0.08 1.5 4.2 29132
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 2.3 2.36 99.4
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 3BXI 2.3 20 28188 932 99.2 0.1433 0.14157 0.151 0.19433 0.1936 RANDOM 33.809
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] 0.42 -0.76 -0.39 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.065 r_dihedral_angle_3_deg 16.874 r_dihedral_angle_4_deg 15.803 r_long_range_B_refined 11.369 r_long_range_B_other 11.369 r_dihedral_angle_1_deg 7.052 r_scangle_other 6.258 r_mcangle_other 6.177 r_mcangle_it 6.175 r_scbond_it 3.645
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.065 r_dihedral_angle_3_deg 16.874 r_dihedral_angle_4_deg 15.803 r_long_range_B_refined 11.369 r_long_range_B_other 11.369 r_dihedral_angle_1_deg 7.052 r_scangle_other 6.258 r_mcangle_other 6.177 r_mcangle_it 6.175 r_scbond_it 3.645 r_scbond_other 3.645 r_mcbond_it 3.578 r_mcbond_other 3.555 r_angle_refined_deg 1.899 r_angle_other_deg 1.151 r_chiral_restr 0.123 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 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 4774 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling MOLREP phasing