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Nitrite-bound MSOX movie series dataset 8 (6.4 MGy) of the copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) - nitrite/NO intermediate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZCN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 297 1.8 M (NH4)2SO2 and 50mM HEPES buffer pH 5
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.881 α = 90 b = 106.881 β = 90 c = 106.881 γ = 90
Symmetry Space Group P 21 3
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 2021-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.99999 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.17 75.58 99.6 0.039 0.999 7.3 5.8 135725 10.57
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.17 1.19 0.831 0.368 0.2 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 7ZCN 1.22 75.58 110618 5985 96.85 0.1306 0.12913 0.1298 0.15826 0.1587 RANDOM 17.264
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.789 r_dihedral_angle_4_deg 20.442 r_dihedral_angle_3_deg 12.574 r_dihedral_angle_1_deg 7.571 r_long_range_B_refined 4.145 r_rigid_bond_restr 3.857 r_scangle_other 3.757 r_long_range_B_other 3.713 r_scbond_it 3.463 r_scbond_other 3.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.789 r_dihedral_angle_4_deg 20.442 r_dihedral_angle_3_deg 12.574 r_dihedral_angle_1_deg 7.571 r_long_range_B_refined 4.145 r_rigid_bond_restr 3.857 r_scangle_other 3.757 r_long_range_B_other 3.713 r_scbond_it 3.463 r_scbond_other 3.256 r_mcangle_other 2.449 r_mcangle_it 2.438 r_angle_refined_deg 2.345 r_mcbond_it 2.014 r_mcbond_other 1.985 r_angle_other_deg 1.62 r_chiral_restr 0.11 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 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 2614 Nucleic Acid Atoms Solvent Atoms 528 Heterogen Atoms 135
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing