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Crystal Structure of Peroxisome Proliferator-Activated Receptor Delta (PPARd) in Complex with a Full Agonist
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 289 15% PEG 8000, 0.2 M KCl, 1 mM EDTA, 25% propanediol, 0.5% heptanetriol, 1 mM DTT, 0.1 M Hepes, pH 7.5, vapor diffusion, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.81 56.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.577 α = 90 b = 92.129 β = 90 c = 39.555 γ = 90
Symmetry Space Group P 21 21 2
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 315 3X3 CCD ARRAY 2004-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.541 ALS 5.0.2
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 94.577 99.8 0.09 0.09 6.225 5.6 24154 24127 2 23.917
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) 2 2.11 99.5 0.37 0.37 2 5.3 3434
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2 94.49 2 24154 24127 1233 99.74 0.192 0.189 0.1884 0.245 0.2447 RANDOM 31.825
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] -1.72 2.71 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.365 r_dihedral_angle_3_deg 17.791 r_dihedral_angle_4_deg 17.154 r_dihedral_angle_1_deg 6.474 r_scangle_it 5.418 r_scbond_it 3.639 r_mcangle_it 2.354 r_angle_refined_deg 2.202 r_mcbond_it 1.396 r_chiral_restr 0.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.365 r_dihedral_angle_3_deg 17.791 r_dihedral_angle_4_deg 17.154 r_dihedral_angle_1_deg 6.474 r_scangle_it 5.418 r_scbond_it 3.639 r_mcangle_it 2.354 r_angle_refined_deg 2.202 r_mcbond_it 1.396 r_chiral_restr 0.139 r_bond_refined_d 0.026 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2115 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 55
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection