4PUA
Crystal Structure Of glutathione transferase YghU from Streptococcus pneumoniae ATCC 700669, complexed with glutathione, Target EFI-507284
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 273 | 0.2 M sodium tartrate dibasic, 20% w/v PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 47.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 55.033 | α = 90 |
b = 59.887 | β = 90 |
c = 170.126 | γ = 90 |
Symmetry | |
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Space Group | I 2 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 | 2014-02-07 | 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) | 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 | 1.708 | 85.063 | 98.8 | 0.083 | 11.5 | 6.8 | 30558 | 30529 |
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 | 1.708 | 1.8 | 97.5 | 1.363 | 2 | 6 | 4317 |
Refinement
Statistics | |||||||||||||||||||
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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 4MZW | 1.708 | 85.06 | 28946 | 1545 | 98.34 | 0.1894 | 0.18694 | 0.23678 | RANDOM | 24.741 |
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] | |
-0.36 | -2.07 | 2.43 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.185 |
r_dihedral_angle_4_deg | 15.605 |
r_dihedral_angle_3_deg | 12.839 |
r_dihedral_angle_1_deg | 6.204 |
r_long_range_B_refined | 5.514 |
r_long_range_B_other | 5.513 |
r_scangle_other | 4.295 |
r_mcangle_it | 3.093 |
r_mcangle_other | 3.093 |
r_scbond_it | 2.793 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2078 |
Nucleic Acid Atoms | |
Solvent Atoms | 116 |
Heterogen Atoms | 40 |
Software
Software | |
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Software Name | Purpose |
MAR345 | data collection |
MOLREP | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALA | data scaling |