3FU5
Leukotriene A4 hydrolase in complex with (5-thiophen-2-ylthiophen-2-yl)methylamine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3FH7 | PDB entry 3FH7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 289 | 13% PEG 8000, 100 mM Imidazole pH 6.5, 100 mM Na Acetate, 5 mM YbCl3, crystal soaked in 13% PEG 8000, 100 mM Imidazole, 100 mM Sodium acetate, 150 mM NaCl, 25 mM 5-thiophen-2-ylthiophen-2-yl)methylamine, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.45 | 49.86 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.403 | α = 90 |
b = 87.226 | β = 90 |
c = 99.521 | 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 | CCD | RIGAKU SATURN 944 | 2008-08-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54178 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.3 | 50 | 97.3 | 0.237 | 4 | 2.9 | 29988 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.3 | 2.38 | 97.2 | 0.785 | 2.7 |
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 | PDB entry 3FH7 | 2.3 | 50 | 29941 | 1504 | 0.211 | 0.208 | 0.255 | RANDOM | 18.57 |
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] | |
0.15 | -0.72 | 0.57 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.253 |
r_dihedral_angle_4_deg | 16.017 |
r_dihedral_angle_3_deg | 13.868 |
r_dihedral_angle_1_deg | 6.111 |
r_scangle_it | 2.418 |
r_scbond_it | 1.453 |
r_angle_refined_deg | 1.387 |
r_mcangle_it | 0.785 |
r_mcbond_it | 0.407 |
r_chiral_restr | 0.084 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4844 |
Nucleic Acid Atoms | |
Solvent Atoms | 223 |
Heterogen Atoms | 28 |
Software
Software | |
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Software Name | Purpose |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |