4KY4
Crystal structure of non-classical TS inhibitor 2 in complex with Toxoplasma gondii TS-DHFR
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4EIL | PDB ENTRY 4EIL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.3 | 293 | 18% PEG 3350, 0.1 M Potassium Formate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.49 | 50.51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.539 | α = 89.97 |
b = 145.122 | β = 89.95 |
c = 176.159 | γ = 89.89 |
Symmetry | |
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Space Group | P 1 |
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 | PIXEL | PSI PILATUS 6M | 2012-11-04 | M | SINGLE WAVELENGTH | |||||||
2 | 1 | x-ray | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X25 | 1.1 | NSLS | X25 |
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 | |||||||||
1,2 | 2.79 | 48.28 | 94.34 | 128608 | 121332 | 2 | 2 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 4EIL | 2.79 | 48.28 | 2 | 128608 | 121332 | 6475 | 97.77 | 0.2222 | 0.2222 | 0.2198 | 0.2676 | RANDOM | 79.025 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-1.1 | 0.25 | -3.58 | -0.25 | 4.67 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.737 |
r_dihedral_angle_4_deg | 20.301 |
r_dihedral_angle_3_deg | 19.366 |
r_mcangle_it | 7.641 |
r_dihedral_angle_1_deg | 7.06 |
r_mcbond_it | 5.164 |
r_mcbond_other | 5.164 |
r_angle_refined_deg | 1.636 |
r_angle_other_deg | 0.961 |
r_chiral_restr | 0.089 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 31444 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 976 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
HKL-2000 | data reduction |
PHASER | phasing |