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High pH (8.0) nitrite-bound MSOX movie series dataset 10 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [6.9 MGy]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8RYR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 100 mM Tris pH 7.3, 1.8 M Ammonium Sulphate
Crystal Properties Matthews coefficient Solvent content 2.55 51.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.3 α = 90 b = 104.3 β = 90 c = 64.47 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2023-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.77491 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.45 45.204 100 0.082 0.101 0.058 0.997 9.4 5.5 70743
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.47 0.999 1.281 0.785 0.392 4.3
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 1.45 45.204 70722 3653 99.96 0.142 0.1403 0.1404 0.1643 0.1638 20.598
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] -0.087 -0.043 -0.087 0.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.776 r_dihedral_angle_3_deg 11.74 r_dihedral_angle_2_deg 9.64 r_dihedral_angle_1_deg 7.723 r_lrange_other 5.903 r_lrange_it 5.901 r_scangle_it 4.13 r_scangle_other 4.129 r_scbond_it 2.817 r_scbond_other 2.816
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.776 r_dihedral_angle_3_deg 11.74 r_dihedral_angle_2_deg 9.64 r_dihedral_angle_1_deg 7.723 r_lrange_other 5.903 r_lrange_it 5.901 r_scangle_it 4.13 r_scangle_other 4.129 r_scbond_it 2.817 r_scbond_other 2.816 r_mcangle_other 2.661 r_mcangle_it 2.659 r_angle_refined_deg 1.932 r_mcbond_it 1.844 r_mcbond_other 1.836 r_angle_other_deg 0.637 r_nbd_refined 0.257 r_symmetry_xyhbond_nbd_refined 0.243 r_xyhbond_nbd_refined 0.192 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.176 r_symmetry_nbd_refined 0.169 r_nbd_other 0.147 r_metal_ion_refined 0.127 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.086 r_symmetry_xyhbond_nbd_other 0.048 r_xyhbond_nbd_other 0.018 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2562 Nucleic Acid Atoms Solvent Atoms 419 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling REFMAC phasing