Neutron structure of copper amine oxidase from Arthrobacter globiformis anaerobically reduced by phenylethylamine at pD 9.0
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | MICRODIALYSIS | | 289 | 1.05 M potassium-sodium tartrate in 25 mM HEPES buffer, pH 7.4. |
Crystal Properties |
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Matthews coefficient | Solvent content |
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3.03 | 59.35 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 157.22 | α = 90 |
b = 62.144 | β = 112.22 |
c = 92.344 | γ = 90 |
Symmetry |
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Space Group | C 1 2 1 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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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 |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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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 |
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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 |
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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 |
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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) |
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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 |
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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 | R-Free | R-Free Selection Details | Mean Isotropic B |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.09 | 44.55 | | | | 337074 | 4636 | 96.8 | | 0.1518 | 0.1513 | 0.1608 | | |
NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.67 | 21.37 | | | | 92709 | | 96.8 | | 0.1995 | 0.1981 | 0.2252 | | |
Temperature Factor Modeling |
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] |
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| | | | | |
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RMS Deviations |
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Key | Refinement Restraint Deviation |
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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 |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 4876 |
Nucleic Acid Atoms | |
Solvent Atoms | 1009 |
Heterogen Atoms | 11 |
Software
Software |
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Software Name | Purpose |
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PHENIX | refinement |
XDS | data scaling |
XDS | data reduction |
PHASER | phasing |