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Crystal structure of a ternary complex of goat lactoperoxidase with cyanide and iodide ions at 2.4 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 7.2 298 100mM Tris-Hcl, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.43 49.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.197 α = 90 b = 80.811 β = 102.96 c = 77.047 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 2006-10-10 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 2.4 74.54 97.9 24962 23672
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 2.4 2.44 90.1
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2GJ1 2.4 74.54 24962 23672 1274 97.79 0.192 0.182 0.17839 0.22786 RANDOM 27.265
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] 0.46 -0.82 -1.38 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.504 r_dihedral_angle_1_deg 4.448 r_scangle_it 3.942 r_scbond_it 2.381 r_angle_refined_deg 1.98 r_mcangle_it 1.681 r_mcbond_it 0.89 r_symmetry_hbond_refined 0.313 r_nbd_refined 0.26 r_symmetry_vdw_refined 0.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.504 r_dihedral_angle_1_deg 4.448 r_scangle_it 3.942 r_scbond_it 2.381 r_angle_refined_deg 1.98 r_mcangle_it 1.681 r_mcbond_it 0.89 r_symmetry_hbond_refined 0.313 r_nbd_refined 0.26 r_symmetry_vdw_refined 0.212 r_xyhbond_nbd_refined 0.189 r_metal_ion_refined 0.138 r_chiral_restr 0.12 r_bond_refined_d 0.014 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 4753 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 203
Software Software Software Name Purpose REFMAC refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing