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Low pH (5.5) as-isolated MSOX movie series dataset 40 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [22.8 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 = 104.29 α = 90 b = 104.29 β = 90 c = 64.79 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 2022-07-18 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 1.78 52.65 99.6 0.137 0.17 0.099 0.994 8.5 4.9 38372
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 1.78 1.82 1.316 1.637 0.948 0.314 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 1.78 52.199 38353 1926 99.448 0.158 0.1562 0.1648 0.1928 0.1991 28.284
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] -0.289 -0.144 -0.289 0.937
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.234 r_dihedral_angle_3_deg 11.96 r_dihedral_angle_2_deg 9.546 r_dihedral_angle_1_deg 7.419 r_lrange_it 6.895 r_lrange_other 6.663 r_scangle_it 5.143 r_scangle_other 5.089 r_scbond_it 3.338 r_scbond_other 3.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.234 r_dihedral_angle_3_deg 11.96 r_dihedral_angle_2_deg 9.546 r_dihedral_angle_1_deg 7.419 r_lrange_it 6.895 r_lrange_other 6.663 r_scangle_it 5.143 r_scangle_other 5.089 r_scbond_it 3.338 r_scbond_other 3.24 r_mcangle_it 3.085 r_mcangle_other 3.085 r_mcbond_it 2.117 r_mcbond_other 2.117 r_angle_refined_deg 1.666 r_angle_other_deg 0.575 r_symmetry_xyhbond_nbd_refined 0.236 r_nbd_refined 0.195 r_xyhbond_nbd_refined 0.19 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_other 0.157 r_nbd_other 0.143 r_symmetry_nbd_refined 0.114 r_symmetry_nbtor_other 0.087 r_metal_ion_refined 0.086 r_chiral_restr 0.083 r_bond_refined_d 0.008 r_gen_planes_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 2554 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing