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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
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KDT PDB entry 3KDT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298 PEG 4000, Ammonium and magnesium acetate, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.07 40.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.93 α = 90 b = 63.93 β = 90 c = 126.771 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 2004-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.1000 APS 17-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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.07 50 99.9 0.091 0.091 25.1 7.5 30861
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.07 2.14 99.2 0.321 5.6 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB entry 3KDT 2.07 45.22 30819 1551 100 0.181 0.178 0.239 0.2258 RANDOM 21.392
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] 0.18 0.18 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.378 r_dihedral_angle_4_deg 14.017 r_dihedral_angle_3_deg 13.948 r_dihedral_angle_1_deg 4.449 r_scangle_it 2.196 r_scbond_it 1.481 r_angle_refined_deg 1.051 r_mcangle_it 1.046 r_mcbond_it 0.644 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.378 r_dihedral_angle_4_deg 14.017 r_dihedral_angle_3_deg 13.948 r_dihedral_angle_1_deg 4.449 r_scangle_it 2.196 r_scbond_it 1.481 r_angle_refined_deg 1.051 r_mcangle_it 1.046 r_mcbond_it 0.644 r_nbtor_refined 0.296 r_nbd_refined 0.189 r_symmetry_vdw_refined 0.178 r_symmetry_hbond_refined 0.145 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4188 Nucleic Acid Atoms Solvent Atoms 433 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing