6VNT
Tryptophan synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the alpha-site, aminoacrylate at the beta site, and sodium ion at the metal coordination site at 1.25 Angstrom resolution
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 | 293 | 50 mM Bicine-NaOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.56 | 51.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 183.022 | α = 90 |
b = 59.382 | β = 94.92 |
c = 67.322 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | M2 | 2018-08-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 12.3.1 | 1.000014 | ALS | 12.3.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.25 | 91.174 | 94.9 | 0.093 | 0.099 | 0.033 | 10.8 | 7.3 | 187530 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.251 | 1.32 | 87 | 0.707 | 0.707 | 0.836 | 0.442 | 1 | 3.3 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.25 | 36.31 | 177873 | 9485 | 94.6 | 0.154 | 0.1526 | 0.1807 | RANDOM | 20.71 |
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] | |
-2.06 | 0.99 | 2.06 | -0.16 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.014 |
r_dihedral_angle_4_deg | 18.137 |
r_dihedral_angle_3_deg | 12.551 |
r_dihedral_angle_1_deg | 6.251 |
r_angle_refined_deg | 1.215 |
r_rigid_bond_restr | 1.031 |
r_chiral_restr | 0.093 |
r_gen_planes_refined | 0.006 |
r_bond_refined_d | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5009 |
Nucleic Acid Atoms | |
Solvent Atoms | 933 |
Heterogen Atoms | 78 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |
DM | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |