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Low pH (5.5) as-isolated MSOX movie series dataset 1 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [0.57 MGy]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HBE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 290 1.8 M ammonium sulfate with 50 mM Hepes buffer (pH 5.5)
Crystal Properties Matthews coefficient Solvent content 2.54 51.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.89 α = 90 b = 103.89 β = 90 c = 64.49 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 2022-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.85504 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.11 52.42 99 0.069 0.035 0.998 8.9 4.2 154268 10.94
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 1.11 1.13 98.6 1.515 0.843 0.34 0.8 3.7
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.11 52 146576 7659 98.97 0.11827 0.11705 0.1174 0.14139 0.142 RANDOM 16.495
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] -0.31 -0.15 -0.31 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.071 r_dihedral_angle_4_deg 18.56 r_dihedral_angle_3_deg 12.402 r_dihedral_angle_1_deg 7.99 r_rigid_bond_restr 4.096 r_long_range_B_refined 3.65 r_scbond_it 3.477 r_long_range_B_other 2.957 r_scangle_other 2.891 r_scbond_other 2.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.071 r_dihedral_angle_4_deg 18.56 r_dihedral_angle_3_deg 12.402 r_dihedral_angle_1_deg 7.99 r_rigid_bond_restr 4.096 r_long_range_B_refined 3.65 r_scbond_it 3.477 r_long_range_B_other 2.957 r_scangle_other 2.891 r_scbond_other 2.762 r_angle_refined_deg 2.066 r_mcangle_other 1.795 r_mcangle_it 1.782 r_mcbond_it 1.764 r_mcbond_other 1.714 r_angle_other_deg 1.522 r_chiral_restr 0.129 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2553 Nucleic Acid Atoms Solvent Atoms 527 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing