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Crystal structure of PPAR gamma (PPARG) in an 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 27% PEG 3350, 0.15M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.64 53.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.106 α = 90 b = 63.106 β = 90 c = 168.056 γ = 90
Symmetry Space Group P 41 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 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 44.62 100 0.101 0.107 0.029 0.999 19.6 13.8 14070
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 2.48 1.387 1.496 0.394 0.798 2 14.2
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 44.66 13337 674 99.96 0.24064 0.23835 0.2423 0.28194 0.2778 RANDOM 96.467
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] 1.63 1.63 -3.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.836 r_dihedral_angle_4_deg 17.539 r_dihedral_angle_3_deg 14.871 r_long_range_B_other 14.012 r_long_range_B_refined 14.011 r_scangle_other 10.114 r_mcangle_it 9.612 r_mcangle_other 9.609 r_dihedral_angle_1_deg 6.901 r_scbond_it 6.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.836 r_dihedral_angle_4_deg 17.539 r_dihedral_angle_3_deg 14.871 r_long_range_B_other 14.012 r_long_range_B_refined 14.011 r_scangle_other 10.114 r_mcangle_it 9.612 r_mcangle_other 9.609 r_dihedral_angle_1_deg 6.901 r_scbond_it 6.67 r_scbond_other 6.667 r_mcbond_it 6.565 r_mcbond_other 6.548 r_angle_refined_deg 1.122 r_angle_other_deg 1.059 r_chiral_restr 0.043 r_bond_refined_d 0.012 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 2158 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing