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High pH (8.0) nitrite-bound MSOX movie series dataset 2 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [1.38 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 7 293 100 mM Tris pH 7.3, 1.8 M Ammonium Sulphate
Crystal Properties Matthews coefficient Solvent content 2.52 51.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.92 α = 90 b = 103.92 β = 90 c = 64.25 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 PILATUS3 6M 2023-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.7749 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 1.13 45.039 99.6 0.078 0.087 0.038 0.998 8.7 4.4 146809
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.13 1.15 99.2 0.916 0.575 0.449 1.3 3.2
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 1.13 45.004 146783 7537 99.629 0.117 0.1156 0.1339 0.1316 15.997
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] -0.203 -0.101 -0.203 0.658
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 20.116 r_lrange_it 20.115 r_dihedral_angle_6_deg 16.401 r_dihedral_angle_3_deg 12.249 r_dihedral_angle_2_deg 11.989 r_scangle_it 9.418 r_scangle_other 9.416 r_dihedral_angle_1_deg 7.955 r_scbond_it 7.308 r_scbond_other 7.306
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 20.116 r_lrange_it 20.115 r_dihedral_angle_6_deg 16.401 r_dihedral_angle_3_deg 12.249 r_dihedral_angle_2_deg 11.989 r_scangle_it 9.418 r_scangle_other 9.416 r_dihedral_angle_1_deg 7.955 r_scbond_it 7.308 r_scbond_other 7.306 r_mcangle_other 7.135 r_mcangle_it 7.132 r_mcbond_it 5.104 r_mcbond_other 5.098 r_rigid_bond_restr 4.732 r_angle_refined_deg 2.002 r_angle_other_deg 0.716 r_symmetry_xyhbond_nbd_refined 0.289 r_nbd_refined 0.25 r_symmetry_nbd_refined 0.219 r_xyhbond_nbd_refined 0.208 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.179 r_nbd_other 0.171 r_chiral_restr 0.109 r_symmetry_nbtor_other 0.088 r_symmetry_xyhbond_nbd_other 0.062 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_xyhbond_nbd_other 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2558 Nucleic Acid Atoms Solvent Atoms 502 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing