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Structure of the ternary complex of lactoperoxidase with substrate nitric oxide (NO) and product nitrite ion (NO2) at 1.98 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LF7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 Sodium nitrate, PEG
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.052 α = 90 b = 80.342 β = 102.82 c = 76.121 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 81 CCD MARRESEARCH 2013-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.98 35.329 99 0.96 32.4 4.3 43516
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.01 0.92
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.98 35.329 43516 2188 98.261 0.186 0.1829 0.1894 0.2335 0.2356 39.155
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] 0.012 -0.016 0.013 -0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.416 r_dihedral_angle_4_deg 14.723 r_dihedral_angle_3_deg 13.541 r_lrange_it 11.323 r_lrange_other 11.296 r_mcangle_it 7.351 r_mcangle_other 7.351 r_dihedral_angle_1_deg 7.077 r_scangle_it 5.643 r_scangle_other 5.642
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.416 r_dihedral_angle_4_deg 14.723 r_dihedral_angle_3_deg 13.541 r_lrange_it 11.323 r_lrange_other 11.296 r_mcangle_it 7.351 r_mcangle_other 7.351 r_dihedral_angle_1_deg 7.077 r_scangle_it 5.643 r_scangle_other 5.642 r_mcbond_other 4.84 r_mcbond_it 4.838 r_scbond_it 3.717 r_scbond_other 3.716 r_chiral_restr_other 2.771 r_angle_other_deg 2.432 r_angle_refined_deg 1.681 r_metal_ion_refined 0.568 r_nbd_other 0.392 r_symmetry_nbd_refined 0.37 r_symmetry_xyhbond_nbd_other 0.256 r_symmetry_nbd_other 0.227 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.206 r_symmetry_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.171 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.074 r_bond_other_d 0.034 r_gen_planes_other 0.023 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4761 Nucleic Acid Atoms Solvent Atoms 366 Heterogen Atoms 192
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing AUTOMAR data collection BUCCANEER model building