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Crystal structure of human PPAR-gamma-ligand binding domain complexed with an indole-based modulator
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SE-MET PPAR-GAMMA-LBD COMPLEX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.95M Trisodium citrate, 0.1M Tris-HCl pH 8.5, 1mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.52 51.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.148 α = 90 b = 59.859 β = 103.76 c = 118.287 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 ADSC QUANTUM 210 2002-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00000 APS 17-ID
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 2.25 40.34 99 0.09 15.6 5 29974 29681 29.6
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) 2.25 2.35 93.7 0.3533 2.51 3407
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SE-MET PPAR-GAMMA-LBD COMPLEX 2.25 40.34 28327 28327 1402 94.5 0.232 0.232 0.232 0.2317 0.274 0.2731 RANDOM 43.5
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] -8.41 2.34 9.36 -0.95
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.6 c_scangle_it 3.37 c_mcangle_it 2.3 c_scbond_it 2.23 c_mcbond_it 1.45 c_angle_deg 0.9 c_improper_angle_d 0.66 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3792 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 88
Software Software Software Name Purpose CNX refinement ADSC data collection HKL-2000 data reduction SCALEPACK data scaling CNX phasing