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Crystal structure of the complex of goat lactoperoxidase with Nitrate at 3.25 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GJ1
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 2.54 51.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.522 α = 85.3 b = 72.537 β = 84.06 c = 83.983 γ = 75.68
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 278 IMAGE PLATE MARRESEARCH Mirror 2006-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.414
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 3.25 20 95.2 0.154 3.8 19863 19863
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 3.25 3.31 95.8 0.278 1.9
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2GJ1 3.25 20 19863 18734 1008 94.85 0.17214 0.17123 0.16868 0.20343 RANDOM 18.726
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] 2.5 1.82 0.21 -0.85 0.13 -2.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.971 r_dihedral_angle_3_deg 18.537 r_dihedral_angle_4_deg 17.42 r_dihedral_angle_1_deg 4.833 r_scangle_it 3.379 r_mcangle_it 1.919 r_scbond_it 1.916 r_angle_refined_deg 1.59 r_mcbond_it 1.011 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.971 r_dihedral_angle_3_deg 18.537 r_dihedral_angle_4_deg 17.42 r_dihedral_angle_1_deg 4.833 r_scangle_it 3.379 r_mcangle_it 1.919 r_scbond_it 1.916 r_angle_refined_deg 1.59 r_mcbond_it 1.011 r_nbtor_refined 0.323 r_nbd_refined 0.266 r_symmetry_vdw_refined 0.197 r_xyhbond_nbd_refined 0.179 r_symmetry_hbond_refined 0.122 r_chiral_restr 0.108 r_metal_ion_refined 0.106 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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 9508 Nucleic Acid Atoms Solvent Atoms 380 Heterogen Atoms 411
Software Software Software Name Purpose REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling AMoRE phasing