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High pH (8.0) as-isolated MSOX movie series dataset 40 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [14 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 = 104.26 α = 90 b = 104.26 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 0.775 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 1.3 64.66 100 0.163 0.184 0.084 0.998 11.5 9 98197
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 1.3 1.32 1.791 2.049 0.969 0.41 7.6
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 1.3 45.187 98169 5049 99.973 0.119 0.1177 0.1223 0.1434 0.1473 19.224
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 -0.059
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.514 r_dihedral_angle_6_deg 16.216 r_lrange_other 13.827 r_dihedral_angle_3_deg 11.389 r_dihedral_angle_2_deg 10.704 r_scangle_it 9.493 r_scangle_other 9.167 r_dihedral_angle_1_deg 7.508 r_scbond_it 6.609 r_mcangle_other 6.393
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.514 r_dihedral_angle_6_deg 16.216 r_lrange_other 13.827 r_dihedral_angle_3_deg 11.389 r_dihedral_angle_2_deg 10.704 r_scangle_it 9.493 r_scangle_other 9.167 r_dihedral_angle_1_deg 7.508 r_scbond_it 6.609 r_mcangle_other 6.393 r_mcangle_it 6.378 r_scbond_other 6.321 r_mcbond_it 4.546 r_mcbond_other 4.529 r_rigid_bond_restr 3.678 r_angle_refined_deg 1.834 r_angle_other_deg 0.611 r_nbd_refined 0.235 r_xyhbond_nbd_refined 0.222 r_symmetry_xyhbond_nbd_refined 0.218 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.176 r_nbd_other 0.174 r_symmetry_nbd_refined 0.169 r_symmetry_xyhbond_nbd_other 0.165 r_metal_ion_refined 0.124 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.086 r_symmetry_metal_ion_refined 0.016 r_bond_refined_d 0.01 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 472 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing