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Crystal structure of human PPARgamma ligand binding domain Y473E mutant in complex with Darglitazone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PRG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 0.1M MOPS, pH 7.4, 0.8M SODIUM CITRATE
Crystal Properties Matthews coefficient Solvent content 2.69 54.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.071 α = 90 b = 61.591 β = 102.17 c = 120.527 γ = 90
Symmetry Space Group C 1 2 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 6M 2018-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
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 2.4 33.415 98.16 0.02448 0.03462 0.02448 0.999 13.59 2 25861 24.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.486 98.76 0.3615 0.3615 0.774 2
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 THROUGHOUT 1PRG 2.4 33.415 1.35 25841 1999 98.21 0.222 0.2174 0.2234 0.2782 0.2776 32.88
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 7.363 f_angle_d 1.167 f_chiral_restr 0.049 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4075 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 60
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing