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Low-dose (14.9 kGy) structure of copper-containing nitrite reductase from Achromobacter cycloclastes at room temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZU6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.75 293 Crystals were grown using the vapor diffusion hanging drop method with a protein concentration of 10 mg/ml. The reservoir solution consisted of 1.6 M ammonium sulfate and 0.1 M sodium acetate (pH 4.75).
Crystal Properties Matthews coefficient Solvent content 2.07 40.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.472 α = 90 b = 96.472 β = 90 c = 96.472 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 293 PIXEL DECTRIS PILATUS 6M 2025-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM07 0.9795 ESRF BM07
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 1.605 26.756 100 0.04085 0.248 0.074 0.995 7 11.2 39308 19.42
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 1.605 1.633 100 3.652 3.896 1.148 0.333 0.6 11.5
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 1.597 27.865 39824 1986 99.797 0.151 0.1493 0.1622 0.179 0.1844 21.026
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_6_deg 15.07 r_dihedral_angle_3_deg 13.321 r_dihedral_angle_2_deg 8.465 r_dihedral_angle_1_deg 7.874 r_lrange_it 5.312 r_lrange_other 5.249 r_scangle_it 4.208 r_scangle_other 4.208 r_scbond_it 2.719 r_scbond_other 2.714
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.07 r_dihedral_angle_3_deg 13.321 r_dihedral_angle_2_deg 8.465 r_dihedral_angle_1_deg 7.874 r_lrange_it 5.312 r_lrange_other 5.249 r_scangle_it 4.208 r_scangle_other 4.208 r_scbond_it 2.719 r_scbond_other 2.714 r_mcangle_it 2.628 r_mcangle_other 2.627 r_mcbond_it 1.757 r_mcbond_other 1.754 r_angle_refined_deg 1.629 r_angle_other_deg 0.562 r_symmetry_nbd_refined 0.288 r_nbd_other 0.222 r_nbd_refined 0.204 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.157 r_metal_ion_refined 0.141 r_symmetry_xyhbond_nbd_refined 0.14 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2543 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing