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Human PPARgamma ligand binding domain complexed with SB1495
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 6.5 295 60% (v/v) Tacsimate
Crystal Properties Matthews coefficient Solvent content 2.32 46.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.359 α = 90 b = 62.451 β = 90 c = 162.161 γ = 90
Symmetry Space Group P 21 21 21
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 2017-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97933 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 2.85 50 99.5 28.7 5.4 15503
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.9
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 2.85 50 14528 777 99.4 0.23754 0.23601 0.2378 0.26601 0.2665 RANDOM 87.947
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] 3.25 3.36 -6.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.215 r_dihedral_angle_4_deg 16.915 r_dihedral_angle_3_deg 13.687 r_long_range_B_other 12.293 r_long_range_B_refined 12.291 r_scangle_other 8.017 r_mcangle_it 7.677 r_mcangle_other 7.676 r_dihedral_angle_1_deg 5.533 r_scbond_it 4.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.215 r_dihedral_angle_4_deg 16.915 r_dihedral_angle_3_deg 13.687 r_long_range_B_other 12.293 r_long_range_B_refined 12.291 r_scangle_other 8.017 r_mcangle_it 7.677 r_mcangle_other 7.676 r_dihedral_angle_1_deg 5.533 r_scbond_it 4.92 r_scbond_other 4.919 r_mcbond_it 4.812 r_mcbond_other 4.812 r_angle_refined_deg 1.468 r_angle_other_deg 0.987 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.003 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 4691 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing