8CPI
Crystal structure of PPAR gamma (PPARG) in complex with WY-14643
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6TSG |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293.15 | 1.6M ammonium sulfate, 0.1M tris 8.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.67 | 53.95 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 65.595 | ¦Á = 90 |
b = 65.595 | ¦Â = 90 |
c = 157.264 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 43 21 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 | PIXEL | DECTRIS PILATUS 6M | 2021-12-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.00002 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 2.1 | 46.38 | 100 | 0.045 | 0.049 | 0.014 | 1 | 23.5 | 11.8 | 20906 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.1 | 2.17 | 1.085 | 1.181 | 0.323 | 0.833 | 12.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2.1 | 46.38 | 19784 | 1058 | 99.95 | 0.22522 | 0.22207 | 0.28219 | RANDOM | 69.197 |
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] | |
1.21 | 1.21 | -2.43 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.45 |
r_dihedral_angle_4_deg | 23.756 |
r_dihedral_angle_3_deg | 16.116 |
r_long_range_B_other | 7.869 |
r_long_range_B_refined | 7.866 |
r_dihedral_angle_1_deg | 7.553 |
r_scangle_other | 5.506 |
r_mcangle_other | 4.57 |
r_mcangle_it | 4.569 |
r_scbond_it | 3.593 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2224 |
Nucleic Acid Atoms | |
Solvent Atoms | 44 |
Heterogen Atoms | 42 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
XDS | data reduction |
PHASER | phasing |