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Human PPARgamma ligand binding domain complexed with Lobeglitazone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GTO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 296 1.6 M sodium citrate tribasic dihydrate (pH 6.5)
Crystal Properties Matthews coefficient Solvent content 2.79 55.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.959 α = 90 b = 53.168 β = 90 c = 54.856 γ = 90
Symmetry Space Group P 21 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 CCD ADSC QUANTUM 270 2015-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97935 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.15 50 99.8 31 4.5
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 5GTO 2.15 30 20491 1033 99.8 0.20879 0.20772 0.214 0.22832 0.2343 RANDOM 46.324
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] -1.55 1.11 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.184 r_dihedral_angle_4_deg 22.108 r_dihedral_angle_3_deg 14.91 r_long_range_B_refined 7.366 r_long_range_B_other 7.34 r_scangle_other 5.304 r_dihedral_angle_1_deg 4.912 r_mcangle_it 3.953 r_mcangle_other 3.952 r_scbond_it 3.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.184 r_dihedral_angle_4_deg 22.108 r_dihedral_angle_3_deg 14.91 r_long_range_B_refined 7.366 r_long_range_B_other 7.34 r_scangle_other 5.304 r_dihedral_angle_1_deg 4.912 r_mcangle_it 3.953 r_mcangle_other 3.952 r_scbond_it 3.32 r_scbond_other 3.318 r_mcbond_it 2.621 r_mcbond_other 2.62 r_angle_refined_deg 1.494 r_angle_other_deg 1.039 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.004 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 2206 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing