2NW7
Crystal Structure of Tryptophan 2,3-dioxygenase (TDO) from Xanthomonas campestris in complex with ferric heme. Northeast Structural Genomics Target XcR13
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1YW0 | PDB entry 1YW0 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.15 | 293 | 50mM MES, 12% PEG1000, 60mM Manganese chloride, pH 6.15, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.13 | 42.37 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 88.939 | α = 90 |
b = 109.359 | β = 90 |
c = 125.513 | 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 | ADSC QUANTUM 4 | mirrors | 2005-09-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4A | 0.97900 | NSLS | X4A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.6 | 46.43 | 98.7 | 0.13 | 0.093 | 10.4 | 4.4 | 37833 | 37833 | 27.7 |
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) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.6 | 2.69 | 94.4 | 0.368 | 0.268 | 2.74 | 4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | 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 1YW0 | 2.7 | 46.43 | 1 | 32665 | 24715 | 2491 | 72 | 0.257 | 0.257 | 0.263 | RANDOM | 34.5 |
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] | |
-10.11 | -13.88 | 23.99 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 20 |
c_angle_deg | 1.2 |
c_improper_angle_d | 0.83 |
c_bond_d | 0.008 |
c_bond_d_na | |
c_bond_d_prot | |
c_angle_d | |
c_angle_d_na | |
c_angle_d_prot | |
c_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8643 |
Nucleic Acid Atoms | |
Solvent Atoms | 142 |
Heterogen Atoms | 172 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
ADSC | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
COMO | phasing |