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Low pH (5.5) as-isolated MSOX movie series dataset 20 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [11.4 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 = 104.3 α = 90 b = 104.3 β = 90 c = 64.8 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 2023-07-17 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 1.66 52.204 99.6 0.099 0.123 0.071 0.997 9.9 4.9 47245
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 1.66 1.69 1.23 1.523 0.876 0.316 4.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.66 52.204 47221 2444 99.48 0.149 0.1471 0.1854 0.1933 26.392
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] -0.282 -0.141 -0.282 0.913
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.742 r_dihedral_angle_3_deg 11.567 r_dihedral_angle_2_deg 8.488 r_dihedral_angle_1_deg 7.458 r_lrange_other 6.78 r_lrange_it 6.778 r_scangle_it 5.118 r_scangle_other 5.117 r_scbond_it 3.351 r_scbond_other 3.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.742 r_dihedral_angle_3_deg 11.567 r_dihedral_angle_2_deg 8.488 r_dihedral_angle_1_deg 7.458 r_lrange_other 6.78 r_lrange_it 6.778 r_scangle_it 5.118 r_scangle_other 5.117 r_scbond_it 3.351 r_scbond_other 3.35 r_mcangle_it 2.909 r_mcangle_other 2.896 r_mcbond_it 2.09 r_mcbond_other 2.089 r_angle_refined_deg 1.765 r_angle_other_deg 0.611 r_symmetry_xyhbond_nbd_refined 0.302 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.225 r_symmetry_nbd_refined 0.193 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.177 r_symmetry_xyhbond_nbd_other 0.168 r_nbd_other 0.16 r_metal_ion_refined 0.093 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 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 362 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing