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Human peroxisome proliferator-activated receptor (PPAR) delta ligand binding domain in complex with a synthetic alpha/delta dual agonist JKPL38
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZNP
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
Crystal Properties Matthews coefficient Solvent content 2.82 56.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.5 α = 90 b = 94.314 β = 97.372 c = 96.247 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 PIXEL DECTRIS PILATUS 2M-F 2015-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.2 50 99.1 0.061 0.073 0.039 0.998 12.8 3.4 66164 33.05
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 99.9 0.427 0.511 0.277 0.894 3.1 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2znp 2.2 42.58 0.06 66164 3279 94.71 0.2017 0.2002 0.1982 0.2316 0.2302 40.69
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 Key Refinement Restraint Deviation f_dihedral_angle_d 13.3739 f_angle_d 0.5291 f_chiral_restr 0.0372 f_plane_restr 0.0039 f_bond_d 0.0021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4161 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 100
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing