Neutron structure of copper amine oxidase from Arthrobacter glibiformis at pD 7.4
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 | 7.4 | 289 | 1.05M potassium-sodium tartrate, 25mM HEPES |
Crystal Properties |
---|
Matthews coefficient | Solvent content |
---|
3 | 58.95 |
Crystal Data
Unit Cell |
---|
Length ( Å ) | Angle ( ˚ ) |
---|
a = 157.548 | α = 90 |
b = 61.779 | β = 112.13 |
c = 92.332 | 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 | CCD | ADSC QUANTUM 315r | | 2016-05-31 | M | SINGLE WAVELENGTH |
2 | 1 | neutron | 100 | PIXEL | DECTRIS PILATUS 6M | Ni-Ti supermirror neutron guide Detector: iBIXDetector type: WSF PSD (Wavelength Shift Fiber Position Sensitive Detector) | 2015-11-10 | 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 | 3.0-5.7 | 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 | 1.14 | 50 | 99.4 | 0.069 | | 0.076 | 0.029 | | | 14.8 | 5.2 | | 296297 | | | 16.56 |
2 | 1.72 | 20.94 | 87.4 | | | | 0.1249 | | | 4.99 | 2.6639 | | 203273 | | | 16.56 |
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 | 1.14 | 1.16 | | 0.801 | | 0.95 | 0.504 | 0.703 | | | 3.5 | |
1 | 1.16 | 1.18 | | 0.71 | | 0.841 | 0.446 | 0.746 | | | 3.5 | |
1 | 1.18 | 1.2 | | 0.629 | | 0.746 | 0.394 | 0.775 | | | 3.5 | |
1 | 1.2 | 1.23 | | 0.553 | | 0.654 | 0.344 | 0.828 | | | 3.5 | |
1 | 1.23 | 1.25 | | 0.494 | | 0.584 | 0.307 | 0.862 | | | 3.5 | |
1 | 1.25 | 1.28 | | 0.433 | | 0.511 | 0.269 | 0.889 | | | 3.6 | |
1 | 1.28 | 1.32 | | 0.375 | | 0.443 | 0.233 | 0.912 | | | 3.6 | |
1 | 1.32 | 1.35 | | 0.314 | | 0.371 | 0.194 | 0.932 | | | 3.6 | |
1 | 1.35 | 1.39 | | 0.264 | | 0.311 | 0.163 | 0.951 | | | 3.6 | |
1 | 1.39 | 1.44 | | 0.223 | | 0.263 | 0.138 | 0.964 | | | 3.6 | |
1 | 1.44 | 1.49 | | 0.186 | | 0.22 | 0.115 | 0.973 | | | 3.6 | |
1 | 1.49 | 1.55 | | 0.149 | | 0.176 | 0.093 | 0.981 | | | 3.5 | |
1 | 1.55 | 1.62 | | 0.148 | | 0.163 | 0.067 | 0.988 | | | 5.6 | |
1 | 1.62 | 1.7 | | 0.128 | | 0.138 | 0.052 | 0.992 | | | 7 | |
1 | 1.7 | 1.81 | | 0.104 | | 0.113 | 0.043 | 0.994 | | | 6.9 | |
1 | 1.81 | 1.95 | | 0.085 | | 0.093 | 0.037 | 0.994 | | | 6.6 | |
1 | 1.95 | 2.15 | | 0.081 | | 0.086 | 0.028 | 0.996 | | | 9.6 | |
1 | 2.15 | 2.46 | | 0.071 | | 0.075 | 0.025 | 0.996 | | | 9.5 | |
1 | 2.46 | 3.09 | | 0.063 | | 0.067 | 0.024 | 0.996 | | | 9.1 | |
1 | 3.09 | 50 | | 0.056 | | 0.062 | 0.027 | 0.992 | | | 6.3 | |
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 | R-Free | R-Free Selection Details | Mean Isotropic B |
---|
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.14 | 45.03 | | 1.33 | | 296105 | 14805 | 99.28 | | 0.1684 | 0.1677 | 0.1815 | | 27.8236 |
NEUTRON DIFFRACTION | | 1.72 | 20.951 | | | | 76237 | 3813 | 87.23 | | 0.1815 | 0.18 | 0.2095 | | |
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 | 22.036 |
f_angle_d | 1.318 |
f_chiral_restr | 0.102 |
f_bond_d | 0.009 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement |
---|
Non-Hydrogen Atoms | Number |
---|
Protein Atoms | 4890 |
Nucleic Acid Atoms | |
Solvent Atoms | 2667 |
Heterogen Atoms | 2 |
Software
Software |
---|
Software Name | Purpose |
---|
PHENIX | refinement |
HKL-2000 | data scaling |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
PHASER | phasing |