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Covalent bond formation between ynone moiety of synthetic fatty acid and hPPARg-LBD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VV3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M Tris-HCl pH 7.4, 0.8 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.61 52.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.89 α = 90 b = 61.17 β = 102.76 c = 118.48 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 315r 2015-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 45.3 76.3 0.058 0.038 0.995 13.6 3 25142
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 0.14 0.086 0.967
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2VV3 2.2 29.57 23879 1263 75.78 0.23861 0.2348 0.2416 0.30971 0.3147 RANDOM 32.729
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] 0.02 0.03 0.06 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.491 r_dihedral_angle_4_deg 20.608 r_dihedral_angle_3_deg 16.276 r_dihedral_angle_1_deg 5.27 r_long_range_B_refined 4.484 r_long_range_B_other 4.478 r_scangle_other 3.279 r_mcangle_it 2.899 r_mcangle_other 2.899 r_scbond_it 2.264
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.491 r_dihedral_angle_4_deg 20.608 r_dihedral_angle_3_deg 16.276 r_dihedral_angle_1_deg 5.27 r_long_range_B_refined 4.484 r_long_range_B_other 4.478 r_scangle_other 3.279 r_mcangle_it 2.899 r_mcangle_other 2.899 r_scbond_it 2.264 r_scbond_other 2.263 r_mcbond_it 2.022 r_mcbond_other 2.021 r_angle_refined_deg 1.523 r_angle_other_deg 0.993 r_chiral_restr 0.078 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.008 r_bond_other_d 0.006 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3991 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling REFMAC phasing