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Crystal structure of PPARgamma V290M mutant ligand binding domain in complex with farglitazar
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, HANGING DROP 293 0.1M TRIS pH8
0.92-1.2M Sodium Citrate
0.1mM TCEP
0.5 micro molar Farglitazar.
Crystal Properties Matthews coefficient Solvent content 2.62 53.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.96 α = 90 b = 61.24 β = 103.17 c = 118.51 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 CCD MAR CCD 130 mm 2009-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87260 ESRF ID23-2
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 2.1 28.94 99.9 0.07 10.5 3.8 38079 29.16
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 2.1 2.21 100 0.329 3.3 3.8
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1PRG 2.1 28.92 1.34 38055 1902 99.92 0.2021 0.2002 0.2017 0.2366 0.2367 RANDOM 40.01
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 13.6427 f_angle_d 1.0011 f_chiral_restr 0.042 f_bond_d 0.0081 f_plane_restr 0.0066
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4104 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 41
Software Software Software Name Purpose PHENIX refinement REFMAC refinement PDB_EXTRACT data extraction PHASER phasing SCALA data scaling MOSFLM data reduction