4L8E
Crystal structure of a glutathione transferase family member from xenorhabdus nematophila, target efi-507418, with two gsh per subunit
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | sitting drop vapor diffusion | 7 | 298 | Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 5% glycerol, 5 mM GSH); Reservoir (0.1 M Sodium Acetate, 0.1 M MES pH 6.5, 30 %(w/v) PEG 400); Cryoprotection (reservoir), sitting drop vapor diffusion, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.45 | 49.75 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 65.331 | α = 90 |
b = 65.331 | β = 90 |
c = 213.919 | γ = 120 |
Symmetry | |
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Space Group | P 65 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 | 100 | CCD | RAYONIX MX225HE | MIRRORS | 2013-06-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.9793 | APS | 31-ID |
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 | 1.7 | 213.919 | 97.6 | 0.117 | 0.117 | 18.2 | 21.4 | 29857 | 29857 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | ||||||||||
1 | 1.7 | 1.79 | 96.7 | 0.01 | 1.003 | 0.8 | 21.9 | 4218 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution 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 | PDB ENTRY 3GX0 | 1.7 | 28.045 | 1.33 | 29592 | 29592 | 1501 | 96.02 | 0.152 | 0.152 | 0.1507 | 0.1759 | RANDOM | 26.8567 |
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 |
f_dihedral_angle_d | 14.304 |
f_angle_d | 1.381 |
f_chiral_restr | 0.085 |
f_bond_d | 0.011 |
f_plane_restr | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1650 |
Nucleic Acid Atoms | |
Solvent Atoms | 199 |
Heterogen Atoms | 67 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
AMoRE | phasing |