6KEL
Crystal structure of Drosophila melanogaster Noppera-bo, glutathione S-transferase epsilon 14 (DmGSTE14), in apo-form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4PNG |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.4 | 293 | 27.5% (w/v) PEG 3350, 100 mM MES-NaOH, and pH 5.4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.31 | 46.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.73 | α = 90 |
b = 76.75 | β = 90 |
c = 104.82 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 95 | PIXEL | DECTRIS EIGER X 4M | 2015-12-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-1A | 1.10000 | Photon Factory | BL-1A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.4 | 46.64 | 96 | 0.095 | 0.098 | 23.2 | 13.6 | 91281 | 13.16 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.4 | 1.45 | 91.4 | 0.662 | 0.694 | 0.717 | 3.31 | 11.2 |
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 (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 | FREE R-VALUE | 4PNG | 1.4 | 46.64 | 1.38 | 91277 | 2000 | 96.45 | 0.1569 | 0.1564 | 0.1799 | Random selection | 18.18 |
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 | 5.8578 |
f_angle_d | 1.265 |
f_chiral_restr | 0.0921 |
f_bond_d | 0.0135 |
f_plane_restr | 0.0087 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3593 |
Nucleic Acid Atoms | |
Solvent Atoms | 536 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PHENIX | model building |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |
ARP/wARP | model building |
Coot | model building |