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Crystal structure of the complex of Lactoperoxidase with Nitric oxide at 2.50A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LRN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 0.2M cacl2, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.3 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.731 α = 90 b = 93.173 β = 91.2 c = 82.319 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 100 CCD MARMOSAIC 225 mm CCD 2019-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.97947 RRCAT INDUS-2 PX-BL21
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.5 48.911 99 0.078 0.997 7.8 3.9 42834
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 98.7 0.806 0.638 1.2 3.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6LRN 2.5 48.864 42372 2105 98.924 0.222 0.219 0.2189 0.2774 0.2751 59.307
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] -0.154 -0.015 -0.088 0.243
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.804 r_dihedral_angle_3_deg 16.038 r_dihedral_angle_4_deg 14.488 r_lrange_it 12.434 r_lrange_other 12.434 r_dihedral_angle_1_deg 7.749 r_mcangle_it 7.285 r_mcangle_other 7.284 r_scangle_it 6.353 r_scangle_other 6.353
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.804 r_dihedral_angle_3_deg 16.038 r_dihedral_angle_4_deg 14.488 r_lrange_it 12.434 r_lrange_other 12.434 r_dihedral_angle_1_deg 7.749 r_mcangle_it 7.285 r_mcangle_other 7.284 r_scangle_it 6.353 r_scangle_other 6.353 r_mcbond_it 4.569 r_mcbond_other 4.568 r_scbond_it 3.939 r_scbond_other 3.938 r_angle_other_deg 2.453 r_angle_refined_deg 1.506 r_symmetry_nbd_refined 0.241 r_symmetry_nbd_other 0.218 r_nbd_other 0.21 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.161 r_metal_ion_refined 0.146 r_ncsr_local_group_1 0.093 r_symmetry_xyhbond_nbd_other 0.088 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.06 r_symmetry_xyhbond_nbd_refined 0.057 r_bond_other_d 0.034 r_gen_planes_other 0.019 r_gen_planes_refined 0.007 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9542 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 259
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing