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Crystal structure of PPAR gamma (PPARG) in complex with WY-14643 (inactive form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TSG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 30% PEG 3350, 0.15M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.63 53.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.521 α = 90 b = 63.355 β = 90 c = 168.355 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 PIXEL DECTRIS PILATUS 6M 2021-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00002 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.4 44.5 99.8 0.058 0.063 0.02 1 17.2 9.6 26908
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.51 1.255 1.409 0.455 0.738 1.8 9.4
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 2.4 44.54 25555 1298 99.68 0.21886 0.21638 0.2155 0.26341 0.2619 RANDOM 89.352
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] 3.23 1.6 -4.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.818 r_dihedral_angle_4_deg 17.642 r_dihedral_angle_3_deg 16.585 r_long_range_B_refined 10.028 r_long_range_B_other 10.028 r_scangle_other 7.603 r_dihedral_angle_1_deg 7.222 r_mcangle_it 6.484 r_mcangle_other 6.483 r_scbond_it 5.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.818 r_dihedral_angle_4_deg 17.642 r_dihedral_angle_3_deg 16.585 r_long_range_B_refined 10.028 r_long_range_B_other 10.028 r_scangle_other 7.603 r_dihedral_angle_1_deg 7.222 r_mcangle_it 6.484 r_mcangle_other 6.483 r_scbond_it 5.106 r_scbond_other 5.104 r_mcbond_it 4.438 r_mcbond_other 4.437 r_angle_refined_deg 1.326 r_angle_other_deg 1.2 r_chiral_restr 0.06 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 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 4222 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing