6A6P

Crystal Structure of Peroxisome Proliferator-Activated Receptor Delta (PPARd)LBD in Complex with DN003316


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5U3R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIQUID DIFFUSION6.5291.150.2~0.3M Sodium flouride, 0.1M MES(pH 6.5)
Crystal Properties
Matthews coefficientSolvent content
2.9758.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.605α = 90
b = 95.749β = 97.91
c = 96.936γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2018-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)0.97960PAL/PLS5C (4A)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.15098.340.102419.015.341153
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.14

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5U3R2.138.2011.3841144202598.360.19530.19360.2278
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.165
f_angle_d0.994
f_chiral_restr0.054
f_bond_d0.008
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4285
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms182

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PHENIXmodel building