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Low pH (5.5) as-isolated MSOX movie series dataset 10 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [5.7 MGy]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8R8S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 50 mM Hepes pH 5.5, 1.8 M Ammonium Sulphate
Crystal Properties Matthews coefficient Solvent content 2.52 51.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.22 α = 90 b = 104.22 β = 90 c = 64.72 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 2022-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.855 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 1.42 52.164 99.5 0.063 0.078 0.045 0.998 10.8 4.6 75045
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 1.42 1.44 1.487 1.819 1.018 0.338 3.8
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 1.42 52.164 75019 3794 99.376 0.147 0.1456 0.1438 0.171 0.1698 21.609
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] -0.281 -0.141 -0.281 0.913
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.791 r_dihedral_angle_3_deg 11.483 r_dihedral_angle_2_deg 10.275 r_dihedral_angle_1_deg 7.518 r_lrange_it 6.093 r_lrange_other 6.093 r_scangle_it 4.309 r_scangle_other 4.308 r_scbond_it 2.822 r_scbond_other 2.822
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.791 r_dihedral_angle_3_deg 11.483 r_dihedral_angle_2_deg 10.275 r_dihedral_angle_1_deg 7.518 r_lrange_it 6.093 r_lrange_other 6.093 r_scangle_it 4.309 r_scangle_other 4.308 r_scbond_it 2.822 r_scbond_other 2.822 r_mcangle_it 2.72 r_mcangle_other 2.692 r_mcbond_it 1.966 r_mcbond_other 1.966 r_angle_refined_deg 1.905 r_angle_other_deg 0.642 r_symmetry_xyhbond_nbd_refined 0.305 r_xyhbond_nbd_refined 0.223 r_symmetry_nbd_refined 0.219 r_nbd_refined 0.208 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.178 r_nbd_other 0.171 r_symmetry_xyhbond_nbd_other 0.133 r_metal_ion_refined 0.111 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.087 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 2561 Nucleic Acid Atoms Solvent Atoms 436 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing