☰ Navigation Tabs
Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and ZINC5672437
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ONI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2M Ammonium sulfate, 0.1M MES, pH 6.5, 30% w/v, PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.19 43.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.054 α = 90 b = 61.054 β = 90 c = 159.29 γ = 90
Symmetry Space Group P 41 21 2
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 PILATUS 6M 2019-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
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 1.8 37.95 99.94 0.02036 0.02879 0.02036 0.999 19.45 2 28829 23.21
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.864 0.1618 0.2288 0.1618 0.928 3.89
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 1.8 37.95 1.34 28822 1999 99.96 0.203 0.2007 0.2074 0.2343 0.2393
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 3.966 f_angle_d 0.869 f_chiral_restr 0.045 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2230 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 21
Software Software Software Name Purpose SCALA data scaling PHENIX refinement DIALS data reduction PHASER phasing