4HPJ
Crystal structure of Tryptophan Synthase at 1.45 A resolution in complex with 2-aminophenol quinonoid in the beta site and the F9 inhibitor in the alpha site
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1TJP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.8 | 298 | 50 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.59 | 52.44 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 184.329 | α = 90 |
b = 59.716 | β = 94.68 |
c = 67.527 | 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 315 | 2012-05-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 12.3.1 | 1.000 | ALS | 12.3.1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.449 | 91.858 | 84.8 | 0.095 | 13.1 | 7.7 | 109585 | 109585 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.45 | 1.53 | 62.9 | 0.447 | 0.447 | 1.6 | 2.6 | 11872 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1TJP | 1.45 | 19.67 | 117892 | 109556 | 5519 | 84.55 | 0.1488 | 0.1488 | 0.1466 | 0.1893 | RANDOM | 19.7331 |
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] | |
-0.08 | 0.07 | 0.13 | -0.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.538 |
r_sphericity_free | 26.666 |
r_dihedral_angle_4_deg | 16.758 |
r_dihedral_angle_3_deg | 12.474 |
r_sphericity_bonded | 11.528 |
r_dihedral_angle_1_deg | 5.648 |
r_rigid_bond_restr | 2.805 |
r_angle_refined_deg | 1.453 |
r_chiral_restr | 0.097 |
r_bond_refined_d | 0.011 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5009 |
Nucleic Acid Atoms | |
Solvent Atoms | 644 |
Heterogen Atoms | 99 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |