2Q6S
2.4 angstrom crystal structure of PPAR gamma complexed to BVT.13 without co-activator peptides
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1KNU | PDB entry 1KNU |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 298 | 1.4M sodium citrate, 0.125 M Tris 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.64 | 53.41 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 92.348 | α = 90 |
b = 62.033 | β = 102.29 |
c = 118.132 | 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 | MARMOSAIC 300 mm CCD | mirrors | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 0.9764 | APS | 22-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.4 | 15 | 91.4 | 0.056 | 0.056 | 26.8 | 6.3 | 23288 | 23288 | 59.22 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.4 | 2.49 | 59.1 | 0.173 | 0.173 | 0.076 | 4 | 1486 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 1KNU | 2.4 | 10 | 22984 | 22984 | 2273 | 90.58 | 0.212 | 0.206 | 0.264 | RANDOM | 40.708 |
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] | |
0.65 | -0.13 | 4.37 | -5.07 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.91 |
r_dihedral_angle_4_deg | 19.438 |
r_dihedral_angle_3_deg | 16.812 |
r_dihedral_angle_1_deg | 5.105 |
r_scangle_it | 4.999 |
r_scbond_it | 3.576 |
r_mcangle_it | 2.626 |
r_mcbond_it | 2.087 |
r_angle_refined_deg | 1.276 |
r_nbtor_refined | 0.303 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4061 |
Nucleic Acid Atoms | |
Solvent Atoms | 151 |
Heterogen Atoms | 27 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
HKL-2000 | data reduction |
MOLREP | phasing |