7TED
Human Ornithine Aminotransferase cocrystallized with its inhibitor, (S,E)-3-amino-4-(fluoromethylene)cyclopent-1-ene-1-carboxylate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1OAT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.8 | 293 | After purification, OAT was buffer exchanged into the crystallization buffer (50 mM Tricine pH 7.8) supplied supplemented with 1 mM 2-ketoglutarate. The protein was concentrated to 6.5 mg/mL. Previously reported crystallization conditions were optimized using the hanging drop vapor diffusion method by varying PEG 6000 (8-12%), NaCl (100-250 mM), and glycerol (0%-10%) with 100 mM Tricine pH 7.8 was being kept constant as the buffer. For each hanging drop, 2 uL of protein solution was mixed with an equal volume of well solution and 0.5 uL of ligand. The crystals with the best morphology and size grew in a final condition containing 12% PEG 6000, 200 mM NaCl, 10% glycerol, and 100 mM Tricine pH 7.8. Crystals were transferred to a cryo-protectant solution (well solution supplemented with 30% glycerol) and flash-frozen in liquid nitrogen |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.65 | 53.54 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 200.11 | α = 90 |
b = 115.43 | β = 94.85 |
c = 185.76 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | PIXEL | DECTRIS EIGER X 9M | 2020-12-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.127 | APS | 21-ID-D |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.63 | 43.73 | 98.9 | 0.987 | 8.2 | 4.7 | 123624 | 46.48 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.63 | 2.7 | 0.294 | 1.7 |
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 | 1OAT | 2.63 | 43.4 | 1.36 | 123606 | 6092 | 98.8 | 0.2815 | 0.2812 | 0.2876 | 18.93 |
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 | 15.0437 |
f_angle_d | 1.5498 |
f_chiral_restr | 0.0953 |
f_bond_d | 0.011 |
f_plane_restr | 0.0061 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 28449 |
Nucleic Acid Atoms | |
Solvent Atoms | 335 |
Heterogen Atoms | 224 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |