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Human PPAR delta ligand binding domain in complex with a synthetic agonist TIPP401
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B50 pdb entry 2b50
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.5 293 14% PEG8000, 200mM KCL, 40mM Bistris ethane, 6% propanediol, 0.5% n-heptyl-beta-D-glucopyranoside, 1mM EDTA, 1mM CaCl2 , pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.73 54.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.172 α = 90 b = 91.947 β = 98.01 c = 96.361 γ = 90
Symmetry Space Group P 1 21 1
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 RIGAKU JUPITER 210 2008-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.65 50 99 0.093 8.6 3.7 19488 31.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.74 93.3 0.282 3.1 1827
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2b50 2.65 42.35 18668 910 94.5 0.214 0.214 0.2068 0.276 0.2687 RANDOM 31.7
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] 1.86 4.3 10.84 -12.7
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.7 c_scangle_it 2.44 c_mcangle_it 1.83 c_scbond_it 1.57 c_angle_deg 1.3 c_improper_angle_d 1.24 c_mcbond_it 1.09 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.7 c_scangle_it 2.44 c_mcangle_it 1.83 c_scbond_it 1.57 c_angle_deg 1.3 c_improper_angle_d 1.24 c_mcbond_it 1.09 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4214 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 98
Software Software Software Name Purpose CNS refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing