3KDU

Crystal structure of peroxisome proliferator-activatedeceptor alpha (PPARalpha) complex with N-3-((2-(4-Chlorophenyl)-5-methyl-1,3-oxazol-4-yl)methoxy)benzyl)-N-((4-methylphenoxy)carbonyl)glycine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KDTPDB entry 3KDT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION298PEG 4000, Ammonium and magnesium acetate, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0740.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.93α = 90
b = 63.93β = 90
c = 126.771γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102004-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.1000APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.075099.90.0910.09125.17.530861
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.072.1499.20.3215.66.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 3KDT2.0745.223081915511000.1810.1780.239RANDOM21.392
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]
0.180.18-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.378
r_dihedral_angle_4_deg14.017
r_dihedral_angle_3_deg13.948
r_dihedral_angle_1_deg4.449
r_scangle_it2.196
r_scbond_it1.481
r_angle_refined_deg1.051
r_mcangle_it1.046
r_mcbond_it0.644
r_nbtor_refined0.296
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.378
r_dihedral_angle_4_deg14.017
r_dihedral_angle_3_deg13.948
r_dihedral_angle_1_deg4.449
r_scangle_it2.196
r_scbond_it1.481
r_angle_refined_deg1.051
r_mcangle_it1.046
r_mcbond_it0.644
r_nbtor_refined0.296
r_nbd_refined0.189
r_symmetry_vdw_refined0.178
r_symmetry_hbond_refined0.145
r_xyhbond_nbd_refined0.124
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4188
Nucleic Acid Atoms
Solvent Atoms433
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing