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Human PPAR-gamma ligand binding domain in complex with LW90
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QP5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.9M-1.2M sodium citrate tribasic dihydrate, 0.1M sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 2.69 54.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.166 α = 90 b = 61.582 β = 101.82 c = 119.003 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 EIGER X 4M 2024-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.967697 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.2 58.24 97.4 0.994 8.7 2.8 33110 50.76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 0.735 1.5
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 2.2 58.24 1.35 33028 1638 96.87 0.2245 0.2229 0.2233 0.2554 0.2549 67.44
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 9.0842 f_angle_d 1.3619 f_chiral_restr 0.0604 f_plane_restr 0.0109 f_bond_d 0.0088
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4006 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 94
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling MOLREP phasing Coot model building