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Human PPAR alpha ligand binding domain in complex with a 1H-pyrazolo[3,4-b]pyridine-derived compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6KXY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 100 mM HEPES-NaOH, 19-23% PEG 4000, 19-23% 1,2-propanediol
Crystal Properties Matthews coefficient Solvent content 2.13 42.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.647 α = 90 b = 61.305 β = 90 c = 100.651 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER R 4M 2020-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.00 SPring-8 BL26B1
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 1.85 45.65 100 0.081 0.085 0.023 0.998 17.4 13.1 24883 36.4
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 1.85 1.89 100 1.847 1.918 0.511 0.653 13.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.85 38.9 1.35 24828 2490 99.98 0.2355 0.2321 0.2321 0.2651 0.2654 40.32
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 19.2891 f_angle_d 0.5913 f_chiral_restr 0.0425 f_plane_restr 0.0042 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2069 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 29
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHENIX phasing