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Crystal structure of human PPARgamma ligand binding domain (Protein delipidated by denature and refold)
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 Tris, pH 7.4
0.8M SODIUM CITRATE
Crystal Properties Matthews coefficient Solvent content 2.67 53.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.04 α = 90 b = 62.1 β = 102.22 c = 118.85 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 PILATUS3 6M 2016-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.97946 ALS 5.0.2
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 2.27 58.08 99.5 0.03669 0.05188 0.03669 0.997 8.43 2 30849 22.79
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.27 2.351 0.341 0.862 1.58 1.9
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 2.27 58.079 1.35 30715 1539 99.5 0.2202 0.2176 0.2236 0.2706 0.2678 31.3728
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 3.206 f_angle_d 0.967 f_chiral_restr 0.049 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4122 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction DIALS data reduction PHASER phasing