1M9B
Crystal structure of the 26 kDa glutathione S-transferase from Schistosoma japonicum complexed with gamma-glutamyl[S-(2-iodobenzyl)cysteinyl]glycine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1GTA | PDB entry 1GTA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 298 | ammonium sulfate, ethanol, dithiothrietol, threalose, sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.97 | 58.31 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 116.567 | α = 90 |
b = 116.567 | β = 90 |
c = 78.748 | γ = 120 |
Symmetry | |
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Space Group | P 63 2 2 |
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 | 90 | CCD | ADSC QUANTUM 4 | 1996-07-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CHESS BEAMLINE A1 | 0.914 | CHESS | A1 |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.6 | 99 | 96.2 | 0.078 | 21.6 | 5.8 | 9743 | 9743 | -3 | 46 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.6 | 2.69 | 89.4 | 0.689 | 2.4 | 4.6 | 871 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1GTA | 2.6 | 26 | 9507 | 9507 | 937 | 93.6 | 0.231 | 0.275 | RANDOM | 45.6 |
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] | |
5.57 | 8.1 | 5.57 | -11.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 21.4 |
c_scangle_it | 3.89 |
c_scbond_it | 2.86 |
c_mcangle_it | 2.17 |
c_mcbond_it | 1.28 |
c_angle_deg | 1.2 |
c_improper_angle_d | 0.78 |
c_bond_d | 0.007 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1778 |
Nucleic Acid Atoms | |
Solvent Atoms | 68 |
Heterogen Atoms | 28 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
CNS | refinement |