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The X-Ray crystal structure of multicopper oxidase from Sulfurimonas sp.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FQG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 290.15 1% w/v Tryptone, 0.001 M Sodium azide, 0.05 M HEPES sodium pH 7.0, 12% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.32 46.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.636 α = 104.86 b = 103.389 β = 103.96 c = 131.906 γ = 98.35
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 9M 2023-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.9785 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.58 50 96.5 0.984 7.4 3.4 126901
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.58 2.62 14.9
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 2FQG 2.58 39.52 1.96 126669 1994 95.97 0.1921 0.1913 0.1953 0.2398 0.234
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 13.125 f_angle_d 1.348 f_chiral_restr 0.069 f_bond_d 0.01 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28659 Nucleic Acid Atoms Solvent Atoms 444 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing