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High pH (8.0) nitrite-bound MSOX movie series dataset 3 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [2.07 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 193 100 mM Tris pH 7.3, 1.8 M Ammonium Sulphate
Crystal Properties Matthews coefficient Solvent content 2.53 51.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.07 α = 90 b = 104.07 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 2023-02-15 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 1.16 45.104 99.7 0.07 0.087 0.051 0.998 8.4 4.5 136362
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 1.16 1.18 1.114 1.436 0.886 0.313 3.3
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 1.16 45.104 136335 6974 99.682 0.118 0.1172 0.111 0.139 0.1327 16.973
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] -0.133 -0.066 -0.133 0.431
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.05 r_dihedral_angle_6_deg 16.283 r_lrange_other 13.137 r_dihedral_angle_3_deg 11.653 r_dihedral_angle_2_deg 11.204 r_scangle_it 8.81 r_scangle_other 8.257 r_dihedral_angle_1_deg 7.903 r_scbond_it 6.55 r_mcangle_other 6.515
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.05 r_dihedral_angle_6_deg 16.283 r_lrange_other 13.137 r_dihedral_angle_3_deg 11.653 r_dihedral_angle_2_deg 11.204 r_scangle_it 8.81 r_scangle_other 8.257 r_dihedral_angle_1_deg 7.903 r_scbond_it 6.55 r_mcangle_other 6.515 r_mcangle_it 6.507 r_scbond_other 5.857 r_mcbond_it 4.555 r_mcbond_other 4.548 r_rigid_bond_restr 3.886 r_angle_refined_deg 1.868 r_angle_other_deg 0.657 r_nbd_refined 0.263 r_symmetry_xyhbond_nbd_refined 0.249 r_xyhbond_nbd_refined 0.197 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.178 r_symmetry_nbd_refined 0.172 r_nbd_other 0.151 r_chiral_restr 0.104 r_metal_ion_refined 0.102 r_symmetry_nbtor_other 0.087 r_xyhbond_nbd_other 0.054 r_symmetry_metal_ion_refined 0.024 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 2559 Nucleic Acid Atoms Solvent Atoms 494 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing