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D98N/C135A mutant of a copper-containing nitrite reductase in complex with nitrite
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YSO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 0.1 M acetate buffer pH 4.5, 5.0% (w/v) PEG 4000, and 75 mM CuSO4
Crystal Properties Matthews coefficient Solvent content 3.04 59.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.334 α = 90 b = 115.334 β = 90 c = 84.332 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 EIGER X 16M 2021-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.12 43 96.6 0.062 0.037 0.997 9.4 3.4 155451 9.61
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.12 1.14 98.9 0.608 0.39 0.617 2 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4YSO 1.12 32.22 1.97 155413 7719 96.57 0.1033 0.1026 0.1024 0.1169 0.1153 15.3
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 f_dihedral_angle_d 9.4801 f_angle_d 1.0831 f_chiral_restr 0.0902 f_plane_restr 0.0075 f_bond_d 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2320 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 19
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing