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Crystal Structure of PPARgamma Ligand Binding Domain in complex with dibenzooxepine derivative compound-9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 293 0.5M LiCl, 0.1M Tris-HCl pH 8.5, 28% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.21 44.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.73 α = 90 b = 54.338 β = 108.61 c = 66.77 γ = 90
Symmetry Space Group P 1 21 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 315 2009-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 50 99.8 0.17 4.5 3.7 15196
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 100 0.614 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.2 50 14420 762 99.7 0.1874 0.18451 0.1909 0.2399 0.2431 RANDOM 27.867
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] -0.68 -0.6 0.33 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.225 r_dihedral_angle_4_deg 15.942 r_dihedral_angle_3_deg 15.928 r_long_range_B_refined 6.294 r_long_range_B_other 6.293 r_dihedral_angle_1_deg 5.898 r_scangle_other 4.412 r_mcangle_other 3.276 r_mcangle_it 3.273 r_scbond_it 2.745
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.225 r_dihedral_angle_4_deg 15.942 r_dihedral_angle_3_deg 15.928 r_long_range_B_refined 6.294 r_long_range_B_other 6.293 r_dihedral_angle_1_deg 5.898 r_scangle_other 4.412 r_mcangle_other 3.276 r_mcangle_it 3.273 r_scbond_it 2.745 r_scbond_other 2.744 r_mcbond_it 2.094 r_mcbond_other 2.083 r_angle_refined_deg 1.72 r_angle_other_deg 1.027 r_chiral_restr 0.107 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2117 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing PDB_EXTRACT data extraction