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Structure of the complex of bovine lactoperoxidase with its catalyzed product hypothiocyanate ion at 2.3A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CXP PDB ENTRY 1CXP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 298 NaNO3, PEG3350, pH6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.46 50.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.63 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 292 IMAGE PLATE MAR scanner 345 mm plate Mirror 2007-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54132
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 2.3 75.81 99.3 29356 27641
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 2.34 99.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1CXP 2.3 24.46 29356 27641 1477 99.2 0.17096 0.16835 0.1687 0.21803 0.2045 RANDOM 29.265
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] 0.26 -0.81 -0.63 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.75 r_dihedral_angle_1_deg 3.828 r_scangle_it 3.224 r_scbond_it 1.884 r_angle_refined_deg 1.73 r_mcangle_it 1.472 r_mcbond_it 0.77 r_symmetry_vdw_refined 0.276 r_nbd_refined 0.247 r_symmetry_hbond_refined 0.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.75 r_dihedral_angle_1_deg 3.828 r_scangle_it 3.224 r_scbond_it 1.884 r_angle_refined_deg 1.73 r_mcangle_it 1.472 r_mcbond_it 0.77 r_symmetry_vdw_refined 0.276 r_nbd_refined 0.247 r_symmetry_hbond_refined 0.204 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.104 r_metal_ion_refined 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 413 Heterogen Atoms 205
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing