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High pH (8.0) as-isolated MSOX movie series dataset 1 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [0.35 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 2.52 51.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.79 α = 90 b = 103.79 β = 90 c = 64.33 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 2023-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.755 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 89.885 100 0.08 0.091 0.041 0.999 12 8.1 183204
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 1.609 1.879 0.925 0.42 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 89.885 183171 9104 99.965 0.113 0.1118 0.1287 0.1218 14.836
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] -0.149 -0.075 -0.149 0.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.923 r_lrange_it 13.682 r_dihedral_angle_3_deg 11.384 r_dihedral_angle_2_deg 11.13 r_lrange_other 10.659 r_dihedral_angle_1_deg 7.889 r_scangle_it 7.861 r_scangle_other 7.519 r_scbond_it 5.827 r_scbond_other 5.395
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.923 r_lrange_it 13.682 r_dihedral_angle_3_deg 11.384 r_dihedral_angle_2_deg 11.13 r_lrange_other 10.659 r_dihedral_angle_1_deg 7.889 r_scangle_it 7.861 r_scangle_other 7.519 r_scbond_it 5.827 r_scbond_other 5.395 r_mcangle_other 5.179 r_mcangle_it 5.168 r_rigid_bond_restr 4.058 r_mcbond_it 3.816 r_mcbond_other 3.712 r_angle_refined_deg 2.012 r_angle_other_deg 0.673 r_nbd_refined 0.242 r_xyhbond_nbd_refined 0.219 r_symmetry_nbd_other 0.19 r_symmetry_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.18 r_nbd_other 0.18 r_symmetry_nbd_refined 0.148 r_metal_ion_refined 0.109 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.087 r_symmetry_xyhbond_nbd_other 0.037 r_symmetry_metal_ion_refined 0.03 r_bond_refined_d 0.013 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 2559 Nucleic Acid Atoms Solvent Atoms 548 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing