☰ Navigation Tabs
Human PPAR-gamma ligand binding domain in complex with AKGO88
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q5P
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 2.67 53.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.507 α = 90 b = 61.485 β = 101.43 c = 118.914 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 2024-07-09 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 2.65 26.65 99.5 0.991 5.2 7.4 19293 55.78
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 2.65 2.78 0.552
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 2.65 26.65 1.35 19267 994 99.17 0.2115 0.2088 0.2187 0.2582 0.2662 65.03
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 5.8927 f_angle_d 1.099 f_chiral_restr 0.0494 f_bond_d 0.0086 f_plane_restr 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3895 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement PHENIX refinement DIALS data reduction Aimless data scaling MOLREP phasing PDB-REDO refinement Coot model building