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Low pH (5.5) nitrite-bound MSOX movie series dataset 11 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [6.71 MGy] - water ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8RFR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 293 0.1 M Tris pH 7.3, 1.8 M Ammonium SUlphate
Crystal Properties Matthews coefficient Solvent content 2.75 55.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.45 α = 90 b = 104.45 β = 90 c = 64.6 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 0.855 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 1.54 45.23 99.8 0.034 0.999 11 5.4 59250 24.22
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 1.54 1.57 98.6 0.764 0.344 1 4.6
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 1.54 30 56246 2983 99.76 0.14664 0.14535 0.1567 0.17173 0.1838 RANDOM 24.693
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] -0.41 -0.2 -0.41 1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.18 r_dihedral_angle_2_deg 10.091 r_dihedral_angle_1_deg 7.492 r_long_range_B_refined 6.981 r_long_range_B_other 6.733 r_scangle_other 5.557 r_scbond_it 3.661 r_scbond_other 3.642 r_mcangle_other 3.233 r_mcangle_it 3.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.18 r_dihedral_angle_2_deg 10.091 r_dihedral_angle_1_deg 7.492 r_long_range_B_refined 6.981 r_long_range_B_other 6.733 r_scangle_other 5.557 r_scbond_it 3.661 r_scbond_other 3.642 r_mcangle_other 3.233 r_mcangle_it 3.226 r_mcbond_it 2.377 r_mcbond_other 2.376 r_angle_refined_deg 1.934 r_angle_other_deg 0.664 r_chiral_restr 0.098 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2562 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling