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Low-dose (33.3 kGy) structure of copper-containing nitrite reductase from Achromobacter cycloclastes at cryogenic 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 38.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.352 α = 90 b = 95.352 β = 90 c = 95.352 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 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) R Sym 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 1.464 27.53 99.9 0.219 0.23 0.21 0.062 0.997 9.1 11.2 49834
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 1.464 1.489 98.1 2.611 2.306 0.729 0.354 1 9.2
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 1.465 28.75 49728 2493 99.857 0.157 0.1552 0.1556 0.191 0.1911 14.009
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 15.029 r_dihedral_angle_3_deg 12.382 r_dihedral_angle_1_deg 8.18 r_dihedral_angle_2_deg 7.168 r_lrange_it 4.325 r_lrange_other 4.071 r_scangle_it 2.626 r_scangle_other 2.501 r_mcangle_it 1.847 r_mcangle_other 1.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.029 r_dihedral_angle_3_deg 12.382 r_dihedral_angle_1_deg 8.18 r_dihedral_angle_2_deg 7.168 r_lrange_it 4.325 r_lrange_other 4.071 r_scangle_it 2.626 r_scangle_other 2.501 r_mcangle_it 1.847 r_mcangle_other 1.847 r_scbond_it 1.681 r_angle_refined_deg 1.669 r_scbond_other 1.578 r_mcbond_it 1.177 r_mcbond_other 1.177 r_angle_other_deg 0.582 r_nbd_refined 0.212 r_nbd_other 0.209 r_symmetry_xyhbond_nbd_refined 0.195 r_symmetry_nbd_other 0.194 r_symmetry_nbd_refined 0.191 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.155 r_metal_ion_refined 0.117 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.087 r_symmetry_xyhbond_nbd_other 0.012 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 2561 Nucleic Acid Atoms Solvent Atoms 391 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing