3W1A
Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with 5-halogenated orotate derivatives
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2E6F | PDB ENTRY 2E6F |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.2 | 298 | 0.1M Cacodylate, 13% PEG3350, 0.05M Hexaamminecobalt (III) Chloride, 1mM Oxonate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 44.74 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 68.24 | ¦Á = 90 |
b = 71.819 | ¦Â = 90 |
c = 123.775 | ¦Ã = 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 | 77 | CCD | ADSC QUANTUM 210 | 2006-04-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NW12A | 1.0 | Photon Factory | AR-NW12A |
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 | 1.42 | 50 | 98.9 | 0.069 | 8.7 | 6.7 | 113914 | 112625 | -3 |
Refinement
Statistics | |||||||||||||||||||
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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 | PDB ENTRY 2E6F | 1.42 | 32.89 | 115210 | 108146 | 5702 | 98.85 | 0.15108 | 0.15108 | 0.14962 | 0.17902 | RANDOM | 13.351 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.805 |
r_dihedral_angle_4_deg | 18.929 |
r_dihedral_angle_3_deg | 11.78 |
r_dihedral_angle_1_deg | 6.516 |
r_angle_refined_deg | 2.537 |
r_chiral_restr | 0.199 |
r_bond_refined_d | 0.028 |
r_gen_planes_refined | 0.02 |
r_bond_other_d | |
r_angle_other_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4776 |
Nucleic Acid Atoms | |
Solvent Atoms | 745 |
Heterogen Atoms | 129 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |