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Higher-dose (1332 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 38.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.375 α = 90 b = 95.375 β = 90 c = 95.375 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) 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 1.504 28.764 100 0.227 0.206 0.061 0.997 9.4 11.2 46178
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 1.504 1.53 100 3.054 2.032 0.617 0.506 1.2 10.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.5 28.757 46345 2320 99.841 0.155 0.1535 0.1539 0.1877 0.1876 14.682
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 14.999 r_dihedral_angle_3_deg 12.491 r_dihedral_angle_1_deg 8.188 r_dihedral_angle_2_deg 7.717 r_lrange_it 4.643 r_lrange_other 4.348 r_scangle_it 2.956 r_scangle_other 2.833 r_mcangle_it 2.24 r_mcangle_other 2.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.999 r_dihedral_angle_3_deg 12.491 r_dihedral_angle_1_deg 8.188 r_dihedral_angle_2_deg 7.717 r_lrange_it 4.643 r_lrange_other 4.348 r_scangle_it 2.956 r_scangle_other 2.833 r_mcangle_it 2.24 r_mcangle_other 2.24 r_scbond_it 1.892 r_scbond_other 1.797 r_angle_refined_deg 1.652 r_mcbond_it 1.396 r_mcbond_other 1.396 r_angle_other_deg 0.57 r_nbd_refined 0.21 r_nbd_other 0.203 r_symmetry_nbd_other 0.195 r_symmetry_xyhbond_nbd_refined 0.194 r_symmetry_nbd_refined 0.191 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.157 r_metal_ion_refined 0.09 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.086 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 386 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing