4NHW
Crystal structure of glutathione transferase SMc00097 from Sinorhizobium meliloti, target EFI-507275, with one glutathione bound per one protein subunit
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3LSZ | PDB ENTRY 3LSZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6.5 | Protein in 10 mM HEPES, pH 7.5, 150 mM sodium chloride, 5% glycerol, reservoir: 25% PEG3350, 0.1M bis-tris pH 6.5, 0.2M ammonium acetate, 5 mM GSH, cryoprotectant: none, vapor diffusion, sitting drop, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.32 | 46.98 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.306 | α = 87.34 |
b = 62.504 | β = 79.73 |
c = 84.426 | γ = 82.04 |
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 | 100 | CCD | ADSC QUANTUM 315 | MIRRORS | 2013-10-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | NSLS | X29A |
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 | 50 | 96.1 | 0.047 | 10.6 | 2 | 62866 | -5 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2 | 2.03 | 83.6 | 0.6 | 1.1 | 1.8 |
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 | PDB ENTRY 3LSZ | 2 | 50 | 60645 | 1906 | 96.18 | 0.17437 | 0.1728 | 0.22553 | RANDOM | 62.183 |
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] | |
0.56 | -0.59 | -2.71 | -0.23 | -0.2 | -1.37 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.68 |
r_dihedral_angle_4_deg | 17.834 |
r_dihedral_angle_3_deg | 16.037 |
r_long_range_B_other | 13.739 |
r_long_range_B_refined | 13.738 |
r_scangle_other | 13.244 |
r_scbond_it | 12.175 |
r_scbond_other | 12.17 |
r_mcangle_other | 10.915 |
r_mcangle_it | 10.914 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6712 |
Nucleic Acid Atoms | |
Solvent Atoms | 229 |
Heterogen Atoms | 80 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |