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Low pH (5.5) as-isolated MSOX movie series dataset 3 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [1.71 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 = 103.99 α = 90 b = 103.99 β = 90 c = 64.57 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 1.17 52.48 99.1 0.057 0.071 0.04 0.998 9.2 4.3 132306
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 1.17 1.19 1.698 2.092 1.191 0.327 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 1.17 52.049 132275 6668 99.017 0.119 0.1177 0.1098 0.1421 0.1361 18.505
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] -0.337 -0.168 -0.337 1.093
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 18.293 r_lrange_other 18.291 r_dihedral_angle_6_deg 15.695 r_dihedral_angle_3_deg 11.505 r_dihedral_angle_2_deg 11.441 r_scangle_it 9.538 r_scangle_other 9.536 r_dihedral_angle_1_deg 7.676 r_scbond_it 7.254 r_scbond_other 7.252
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 18.293 r_lrange_other 18.291 r_dihedral_angle_6_deg 15.695 r_dihedral_angle_3_deg 11.505 r_dihedral_angle_2_deg 11.441 r_scangle_it 9.538 r_scangle_other 9.536 r_dihedral_angle_1_deg 7.676 r_scbond_it 7.254 r_scbond_other 7.252 r_mcangle_it 6.251 r_mcangle_other 6.242 r_mcbond_it 4.599 r_mcbond_other 4.598 r_rigid_bond_restr 3.748 r_angle_refined_deg 1.855 r_angle_other_deg 0.66 r_symmetry_xyhbond_nbd_refined 0.266 r_nbd_refined 0.244 r_symmetry_nbd_refined 0.223 r_xyhbond_nbd_refined 0.214 r_symmetry_nbd_other 0.187 r_nbd_other 0.18 r_nbtor_refined 0.178 r_metal_ion_refined 0.117 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.087 r_symmetry_xyhbond_nbd_other 0.057 r_symmetry_metal_ion_refined 0.019 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2553 Nucleic Acid Atoms Solvent Atoms 505 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing