5YSO
Crystal structure of Estrogen Related Receptor-3 (ERR-gamma) ligand binding domain with DN200434
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1S9Q |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 291 | 0.2M Ammonium fluoride, 20%(w/v) PEG 3350, 10mM Barium chloride dihydrate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.65 | 53.58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 105.886 | α = 90 |
b = 79.828 | β = 107.81 |
c = 106.714 | 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 | 100 | CCD | ADSC QUANTUM 315r | 2016-04-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PAL/PLS BEAMLINE 5C (4A) | 0.9794 | PAL/PLS | 5C (4A) |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rpim I (All) | CC (Half) | 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 | 2.501 | 50 | 96.49 | 0.043 | 0.975 | 2.6 | 6.8 | 28403 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.501 | 2.591 | 76.67 | 0.141 | 8.2 | 6.9 |
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 | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | NONE | 1S9Q | 2.501 | 43.711 | 1.34 | 28400 | 1411 | 96.51 | 0.1992 | 0.1968 | 0.2434 |
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 | 6.059 |
f_angle_d | 0.938 |
f_chiral_restr | 0.046 |
f_bond_d | 0.008 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5028 |
Nucleic Acid Atoms | |
Solvent Atoms | 225 |
Heterogen Atoms | 102 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-2000 | data processing |
PHENIX | phasing |
HKL-2000 | data scaling |
HKL-2000 | data reduction |