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High pH (8.0) nitrite-bound MSOX movie series dataset 30 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [20.7 MGy]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8RU9
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 = 104.56 α = 90 b = 104.56 β = 90 c = 64.66 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 1.8 45.28 100 0.133 0.165 0.095 0.995 6.8 5.6 37438
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 1.8 1.84 1.23 1.518 0.873 0.365 5.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.8 30.002 37411 1873 99.925 0.153 0.1516 0.1833 0.1922 28.482
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] 0.067 0.034 0.067 -0.218
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.546 r_dihedral_angle_3_deg 11.347 r_dihedral_angle_2_deg 8.798 r_dihedral_angle_1_deg 7.444 r_lrange_other 6.535 r_lrange_it 6.526 r_scangle_it 4.804 r_scangle_other 4.802 r_scbond_it 3.178 r_scbond_other 3.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.546 r_dihedral_angle_3_deg 11.347 r_dihedral_angle_2_deg 8.798 r_dihedral_angle_1_deg 7.444 r_lrange_other 6.535 r_lrange_it 6.526 r_scangle_it 4.804 r_scangle_other 4.802 r_scbond_it 3.178 r_scbond_other 3.178 r_mcangle_it 2.992 r_mcangle_other 2.992 r_mcbond_it 2.11 r_mcbond_other 2.109 r_angle_refined_deg 1.707 r_angle_other_deg 0.553 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.196 r_symmetry_nbd_other 0.189 r_symmetry_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.175 r_nbd_other 0.148 r_symmetry_xyhbond_nbd_other 0.131 r_metal_ion_refined 0.121 r_symmetry_nbd_refined 0.117 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.082 r_xyhbond_nbd_other 0.024 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2558 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement REFMAC refinement REFMAC phasing Aimless data scaling xia2 data reduction