6D0A
Crystal structure of Kynurenine Aminotransferase-II in apo-form, at 1.47 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5EUN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | Protein 10 mg/mL was mixed with an equal volume of a reservoir solution containing 200 mM NaCl, 0.1 M NaCitrate pH 5.6, 24% PEG4K and equilibrated against 1 mL of a reservoir solution. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.37 | 48.05 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 102.765 | α = 90 |
b = 102.765 | β = 90 |
c = 86.498 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | 2017-08-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.9537 | Australian Synchrotron | MX2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (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 | 1.468 | 45.958 | 99.89 | 0.05847 | 0.05963 | 0.01158 | 41.07 | 2 | 79172 | 14.4876525592 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.468 | 1.521 | 98.97 | 0.2693 | 0.2746 | 0.05284 | 11.61 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 5EUN | 1.46809418277 | 45.9579051416 | 1.38369573649 | 79169 | 2000 | 99.8914894959 | 0.173889680561 | 0.173515953791 | 0.187901673544 | 22.030880913 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 11.6047800469 |
f_angle_d | 0.998825040111 |
f_chiral_restr | 0.0762402474895 |
f_bond_d | 0.00869171408715 |
f_plane_restr | 0.00788802967208 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3392 |
Nucleic Acid Atoms | |
Solvent Atoms | 483 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
phenix.refine | refinement |
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
PHENIX | phasing |