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High pH (8.0) as-isolated MSOX movie series dataset 2 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [0.7 MGy]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8S0W
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 = 103.82 α = 90 b = 103.82 β = 90 c = 64.35 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 0.775 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 1.05 64.35 100 0.082 0.093 0.042 0.999 11.8 8.1 183378
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 1.05 1.07 1.732 2.022 0.995 0.386 6.2
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 1.05 52.383 183344 9116 99.995 0.115 0.1147 0.1295 0.1279 16.116
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] 0.018 0.009 0.018 -0.06
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.325 r_dihedral_angle_6_deg 16.24 r_lrange_other 14.529 r_dihedral_angle_2_deg 12.07 r_dihedral_angle_3_deg 11.65 r_scangle_it 8.956 r_scangle_other 8.658 r_mcangle_other 7.879 r_dihedral_angle_1_deg 7.861 r_mcangle_it 7.766
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.325 r_dihedral_angle_6_deg 16.24 r_lrange_other 14.529 r_dihedral_angle_2_deg 12.07 r_dihedral_angle_3_deg 11.65 r_scangle_it 8.956 r_scangle_other 8.658 r_mcangle_other 7.879 r_dihedral_angle_1_deg 7.861 r_mcangle_it 7.766 r_scbond_it 6.321 r_scbond_other 5.936 r_mcbond_it 5.746 r_mcbond_other 5.464 r_rigid_bond_restr 4.069 r_angle_refined_deg 2.002 r_angle_other_deg 0.693 r_nbd_refined 0.251 r_xyhbond_nbd_refined 0.23 r_symmetry_xyhbond_nbd_refined 0.201 r_symmetry_nbd_other 0.193 r_nbd_other 0.183 r_nbtor_refined 0.179 r_symmetry_nbd_refined 0.127 r_chiral_restr 0.105 r_metal_ion_refined 0.093 r_symmetry_nbtor_other 0.088 r_symmetry_xyhbond_nbd_other 0.028 r_symmetry_metal_ion_refined 0.028 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2551 Nucleic Acid Atoms Solvent Atoms 529 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing