5T7O
Crystal structure of Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase in complex with (6S)-5,6,7,8-TETRAHYDROFOLATE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3INV |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 298 | TcDHFR-TS 12.5 mg ml-1 in 25 mMTris pH 7.2 and 80 mMNaCl, precipitant solution 12% (w/v) PEG 3350, 100 mM sodium malonate pH 5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.63 | 53.19 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 154.547 | α = 90 |
b = 173.54 | β = 90 |
c = 174.159 | γ = 90 |
Symmetry | |
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Space Group | I 2 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 6M | 2015-12-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.96861 | Diamond | I24 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.8 | 86.77 | 99.5 | 9.2 | 6.5 | 213627 | 2 |
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 | 3INV | 1.8 | 86.77 | 202617 | 10547 | 99.23 | 0.17906 | 0.1769 | 0.21991 | RANDOM | 26.495 |
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] | |
-0.01 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.032 |
r_dihedral_angle_4_deg | 18.545 |
r_dihedral_angle_3_deg | 14.54 |
r_long_range_B_refined | 7.974 |
r_dihedral_angle_1_deg | 6.481 |
r_scbond_it | 3.828 |
r_mcangle_it | 3.644 |
r_mcbond_it | 2.748 |
r_angle_refined_deg | 2.392 |
r_chiral_restr | 0.202 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15441 |
Nucleic Acid Atoms | |
Solvent Atoms | 2024 |
Heterogen Atoms | 588 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
iMOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |