2PGT
CRYSTAL STRUCTURE OF HUMAN GLUTATHIONE S-TRANSFERASE P1-1[V104] COMPLEXED WITH (9R,10R)-9-(S-GLUTATHIONYL)-10-HYDROXY-9,10-DIHYDROPHENANTHRENE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1PGT | PDB ENTRY 1PGT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | CRYSTALS WERE GROWN IN HANGING DROPS WHICH INITIALLY CONSISTED OF 5.9 MG/ML PROTEIN IN 0.1 M HEPES BUFFER (PH 7.0) CONTAINING 8.3 MM S-HEXYLGLUTATHIONE AND 1.0 M BUFFERED (PH 7.0) AMMONIUM SULFATE. THE DROPS WERE EQUILIBRATED AT 293 K AGAINST WELL SOLUTION CONTAINING BETWEEN 1.9 - 2.0 M AMMONIUM SULFATE IN 0.1 M HEPES BUFFER (PH 7.0)., vapor diffusion - hanging drop |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 80.18 | α = 90 |
b = 90.54 | β = 98.45 |
c = 69.37 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 293 | IMAGE PLATE | RIGAKU RAXIS II | MIRRORS | 1996-04-16 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH2R |
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 | 1.9 | 20 | 95.5 | 0.059 | 12.31 | 3.9 | 40456 | 23.61 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
1.9 | 1.93 | 77.3 | 0.287 | 1.77 | 1.45 |
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-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | DIFFERENCE FOURIER | THROUGHOUT | PDB ENTRY 1PGT | 1.9 | 6 | 3 | 40456 | 30838 | 83 | 0.183 | 26.04 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
p_staggered_tor | 18.2 |
p_transverse_tor | 17.9 |
p_planar_tor | 6.9 |
p_scangle_it | 1.995 |
p_scbond_it | 1.298 |
p_mcangle_it | 1.225 |
p_mcbond_it | 0.726 |
p_singtor_nbd | 0.224 |
p_xyhbond_nbd | 0.217 |
p_chiral_restr | 0.183 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3282 |
Nucleic Acid Atoms | |
Solvent Atoms | 344 |
Heterogen Atoms | 100 |
Software
Software | |
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Software Name | Purpose |
X-PLOR | model building |
GPRLSA | refinement |
X-PLOR | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
X-PLOR | phasing |