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Human PPARgamma ligand binding domain complexed with SB1494
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 7 295 2.2 M sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.83 56.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.197 α = 90 b = 53.324 β = 90 c = 53.837 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 2016-07-07 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 2.15 50 99.9 41 9.8 21339
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 2.15 2.19
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 20210 1019 99.83 0.20566 0.20372 0.215 0.24113 0.2482 RANDOM 54.354
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] -1.56 0.14 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.781 r_dihedral_angle_4_deg 20.579 r_dihedral_angle_3_deg 13.721 r_long_range_B_refined 9.552 r_long_range_B_other 9.548 r_scangle_other 7.536 r_dihedral_angle_1_deg 6.574 r_mcangle_it 5.595 r_mcangle_other 5.593 r_scbond_it 4.967
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.781 r_dihedral_angle_4_deg 20.579 r_dihedral_angle_3_deg 13.721 r_long_range_B_refined 9.552 r_long_range_B_other 9.548 r_scangle_other 7.536 r_dihedral_angle_1_deg 6.574 r_mcangle_it 5.595 r_mcangle_other 5.593 r_scbond_it 4.967 r_scbond_other 4.952 r_mcbond_it 3.887 r_mcbond_other 3.885 r_angle_refined_deg 1.478 r_angle_other_deg 0.496 r_chiral_restr 0.06 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 2208 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing