7L1H
The aminoacrylate form of the wild-type Salmonella typhimurium Tryptophan Synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site at 1.50 Angstrom resolution. Three water molecules are close to the amynoacrylate at the enzyme beta-site
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4HN4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.8 | 298 | 50 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.59 | 52.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 183.97 | α = 90 |
b = 59.73 | β = 94.7 |
c = 67.42 | 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 | IMAGE PLATE | RIGAKU RAXIS IV++ | VariMax HighFlux | 2020-03-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.5 | 91.676 | 89.6 | 0.054 | 0.054 | 0.063 | 0.033 | 11.2 | 3.3 | 104698 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.5 | 1.58 | 44.6 | 0.263 | 0.263 | 0.344 | 0.218 | 2.7 | 2.3 |
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 | 4HN4 | 1.5 | 39.4 | 99207 | 5212 | 89.47 | 0.1405 | 0.1383 | 0.1846 | RANDOM | 23.077 |
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] | |
-0.24 | -0.21 | 0.15 | 0.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.301 |
r_dihedral_angle_4_deg | 17.202 |
r_dihedral_angle_3_deg | 12.69 |
r_dihedral_angle_1_deg | 6.149 |
r_rigid_bond_restr | 1.956 |
r_angle_refined_deg | 1.383 |
r_chiral_restr | 0.097 |
r_gen_planes_refined | 0.008 |
r_bond_refined_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5009 |
Nucleic Acid Atoms | |
Solvent Atoms | 921 |
Heterogen Atoms | 138 |
Software
Software | |
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Software Name | Purpose |
iMOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |
DM | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |