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Crystal structure of PPAR gamma (PPARG) in complex with JP85 (compound 1).
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 8 293.15 1.4 M Ammonium sulfate, 0.1 M tris pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.63 53.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.331 α = 90 b = 65.331 β = 90 c = 156.041 γ = 90
Symmetry Space Group P 43 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 PILATUS3 2M 2019-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00000 SLS X06DA
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 1.9 44.3 99.3 0.059 0.065 0.021 0.999 16.6 8.7 27306
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 1.9 1.97 98.5 0.877 0.987 0.324 0.767 2.2 8.5
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 6TSG 1.9 44.3 25886 1353 98.99 0.1768 0.1755 0.185 0.201 0.209 RANDOM 43.145
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] 0.03 0.03 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.161 r_dihedral_angle_4_deg 14.098 r_dihedral_angle_3_deg 13.735 r_dihedral_angle_1_deg 6.584 r_angle_refined_deg 1.475 r_angle_other_deg 1.383 r_chiral_restr 0.08 r_bond_refined_d 0.015 r_gen_planes_refined 0.014 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.161 r_dihedral_angle_4_deg 14.098 r_dihedral_angle_3_deg 13.735 r_dihedral_angle_1_deg 6.584 r_angle_refined_deg 1.475 r_angle_other_deg 1.383 r_chiral_restr 0.08 r_bond_refined_d 0.015 r_gen_planes_refined 0.014 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2196 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 76
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing