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Higher-dose (283.1 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 33.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.542 α = 90 b = 96.542 β = 90 c = 96.542 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 2.016 29.117 100 0.402 0.417 0.124 0.991 5.8 11.2 20090 28.19
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 2.016 2.051 100 3.65 3.7 1.089 0.35 0.8 11.4 1013
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 2.008 29.109 20270 1004 99.847 0.159 0.1562 0.1658 0.2094 0.2038 30.316
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 14.686 r_dihedral_angle_3_deg 14.083 r_dihedral_angle_2_deg 9.411 r_dihedral_angle_1_deg 8.251 r_lrange_it 6.425 r_lrange_other 6.421 r_scangle_it 4.957 r_scangle_other 4.945 r_mcangle_it 3.513 r_mcangle_other 3.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.686 r_dihedral_angle_3_deg 14.083 r_dihedral_angle_2_deg 9.411 r_dihedral_angle_1_deg 8.251 r_lrange_it 6.425 r_lrange_other 6.421 r_scangle_it 4.957 r_scangle_other 4.945 r_mcangle_it 3.513 r_mcangle_other 3.513 r_scbond_it 3.258 r_scbond_other 3.214 r_mcbond_it 2.372 r_mcbond_other 2.37 r_angle_refined_deg 1.697 r_angle_other_deg 0.812 r_symmetry_nbd_refined 0.206 r_nbd_other 0.206 r_symmetry_nbd_other 0.2 r_nbd_refined 0.197 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.15 r_symmetry_xyhbond_nbd_refined 0.142 r_metal_ion_refined 0.13 r_symmetry_nbtor_other 0.091 r_chiral_restr 0.075 r_symmetry_xyhbond_nbd_other 0.021 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2539 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing