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MSOX movie series dataset 10 (11.5 MGy) for nitrite bound BrJNiR (Cu containing nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 at pH 8.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8RYU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 100 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 = 104.3 α = 90 b = 104.3 β = 90 c = 64.47 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 0.77491 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 1.45 45.204 100 0.082 0.101 0.058 0.997 9.4 5.5 70743
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 1.45 1.47 0.999 1.281 0.785 0.392 4.3
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 1.45 45.204 70722 3653 99.96 0.142 0.1403 0.1404 0.1643 0.1638 20.598
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] -0.087 -0.043 -0.087 0.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.776 r_dihedral_angle_3_deg 11.74 r_dihedral_angle_2_deg 9.64 r_dihedral_angle_1_deg 7.723 r_lrange_other 5.903 r_lrange_it 5.901 r_scangle_it 4.13 r_scangle_other 4.129 r_scbond_it 2.817 r_scbond_other 2.816
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.776 r_dihedral_angle_3_deg 11.74 r_dihedral_angle_2_deg 9.64 r_dihedral_angle_1_deg 7.723 r_lrange_other 5.903 r_lrange_it 5.901 r_scangle_it 4.13 r_scangle_other 4.129 r_scbond_it 2.817 r_scbond_other 2.816 r_mcangle_other 2.661 r_mcangle_it 2.659 r_angle_refined_deg 1.932 r_mcbond_it 1.844 r_mcbond_other 1.836 r_angle_other_deg 0.637 r_nbd_refined 0.257 r_symmetry_xyhbond_nbd_refined 0.243 r_xyhbond_nbd_refined 0.192 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.176 r_symmetry_nbd_refined 0.169 r_nbd_other 0.147 r_metal_ion_refined 0.127 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.086 r_symmetry_xyhbond_nbd_other 0.048 r_xyhbond_nbd_other 0.018 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2562 Nucleic Acid Atoms Solvent Atoms 419 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling REFMAC phasing