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Neutron structure of copper amine oxidase from Arthrobacter globiformis anaerobically reduced by phenylethylamine at pD 9.0
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WA2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 289 1.05 M potassium-sodium tartrate in 25 mM HEPES buffer, pH 7.4.
Crystal Properties Matthews coefficient Solvent content 3.03 59.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.22 α = 90 b = 62.144 β = 112.22 c = 92.344 γ = 90
Symmetry Space Group C 1 2 1
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 2018-05-22 M SINGLE WAVELENGTH 2 1 neutron 100 DIFFRACTOMETER iBIX 2018-04-05 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A 2 SPALLATION SOURCE J-PARC MLF BEAMLINE BL-03 2.716-5.335 JPARC MLF BL-03
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) R Split (All) 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 1.09 50 97.4 0.052 0.062 0.995 9.58 3.238 650618 2 1.67 21.37 96.9 0.1235 4.85 5.5811 92713
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.09 1.16 0.264 0.321 0.948 1 1.16 1.24 0.172 0.208 0.971 1 1.24 1.34 0.123 0.147 0.984 1 1.34 1.47 0.084 0.102 0.989 1 1.47 1.64 0.062 0.073 0.993 1 1.64 1.89 0.05 0.06 0.993 1 1.89 2.32 0.045 0.054 0.994 1 2.32 3.27 0.047 0.056 0.993 1 3.27 50 0.048 0.057 0.992
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 1.09 44.55 337074 4636 96.8 0.1518 0.1513 0.1509 0.1608 0.1607 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 1.67 21.37 92709 96.8 0.1995 0.1981 0.2252
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 17.786 f_angle_d 1.381 f_chiral_restr 0.102 f_plane_restr 0.011 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4876 Nucleic Acid Atoms Solvent Atoms 1009 Heterogen Atoms 11
Software Software Software Name Purpose PHENIX refinement XDS data scaling XDS data reduction PHASER phasing