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High pH (8.0) nitrite-bound MSOX movie series dataset 4 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [2.76 MGy]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8RYJ
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 2.52 51.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.12 α = 90 b = 104.12 β = 90 c = 64.36 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 1.25 45.126 99.8 0.069 0.086 0.05 0.998 9.6 4.8 109422
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 1.25 1.27 0.95 1.237 0.779 0.391 3.5
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 1.25 45.126 109393 5651 99.807 0.109 0.1073 0.1028 0.1309 0.1265 17.691
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] -0.17 -0.085 -0.17 0.551
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 18.064 r_lrange_it 18.063 r_dihedral_angle_6_deg 16.247 r_dihedral_angle_3_deg 11.96 r_dihedral_angle_2_deg 11.269 r_scangle_it 9.266 r_scangle_other 9.264 r_dihedral_angle_1_deg 7.931 r_scbond_it 6.734 r_scbond_other 6.732
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 18.064 r_lrange_it 18.063 r_dihedral_angle_6_deg 16.247 r_dihedral_angle_3_deg 11.96 r_dihedral_angle_2_deg 11.269 r_scangle_it 9.266 r_scangle_other 9.264 r_dihedral_angle_1_deg 7.931 r_scbond_it 6.734 r_scbond_other 6.732 r_mcangle_other 6.664 r_mcangle_it 6.654 r_mcbond_it 4.614 r_mcbond_other 4.598 r_rigid_bond_restr 3.846 r_angle_refined_deg 1.865 r_angle_other_deg 0.645 r_nbd_refined 0.264 r_symmetry_xyhbond_nbd_refined 0.253 r_xyhbond_nbd_refined 0.199 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.176 r_symmetry_nbd_refined 0.176 r_nbd_other 0.149 r_chiral_restr 0.102 r_metal_ion_refined 0.102 r_symmetry_nbtor_other 0.086 r_symmetry_xyhbond_nbd_other 0.014 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_symmetry_metal_ion_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 2562 Nucleic Acid Atoms Solvent Atoms 495 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling REFMAC phasing