8AWH
Leukotriene A4 hydrolase in complex with 4-(4-Benzylphenyl)-selenazol-2-amine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4L2L |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.8 | 293 | 12% PEG 8000, 100 mM sodium acetate, 5 mM ytterbium chloride, 100 mM imidazole pH 6.8 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 48.25 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 77.022 | α = 90 |
b = 87.519 | β = 90 |
c = 99.007 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 16M | 2021-10-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX IV BEAMLINE BioMAX | 0.9763 | MAX IV | BioMAX |
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) | 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 | 1.415 | 43.13 | 95.6 | 0.199 | 0.207 | 0.056 | 0.996 | 11.3 | 13.3 | 76734 |
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) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.415 | 1.606 | 1.917 | 2.007 | 0.59 | 0.996 | 1.838 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4L2L | 1.42 | 43.13 | 72951 | 3783 | 60.09 | 0.1576 | 0.156 | 0.1871 | RANDOM | 17.891 |
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] | |
-0.18 | -0.05 | 0.22 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.861 |
r_dihedral_angle_4_deg | 19.374 |
r_dihedral_angle_3_deg | 13.356 |
r_dihedral_angle_1_deg | 6.519 |
r_angle_refined_deg | 1.572 |
r_angle_other_deg | 1.422 |
r_chiral_restr | 0.084 |
r_bond_refined_d | 0.01 |
r_gen_planes_refined | 0.009 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4853 |
Nucleic Acid Atoms | |
Solvent Atoms | 579 |
Heterogen Atoms | 81 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
PHASER | phasing |
PDB_EXTRACT | data extraction |
STARANISO | data scaling |