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Crystal structure of PPARgamma in complex with compound 16 (MF27)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AVI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293.15 33% PEG 3350, 0.15 M sodium citrate and 0.1 M tris, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.58 52.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.542 α = 90 b = 62.542 β = 90 c = 166.861 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 PILATUS3 6M 2019-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0000 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 2.8 44.22 99.9 0.088 0.102 0.037 0.999 15.8 7 8762
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 2.8 2.95 99.8 0.993 1.154 0.428 0.674 1.9 7
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 6avi 2.8 44.22 8358 377 99.78 0.2341 0.2324 0.2339 0.2714 0.2683 RANDOM 80.872
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] 0.53 0.53 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.159 r_dihedral_angle_4_deg 17.42 r_dihedral_angle_3_deg 15.224 r_dihedral_angle_1_deg 7.272 r_angle_refined_deg 1.129 r_angle_other_deg 1.123 r_chiral_restr 0.051 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.159 r_dihedral_angle_4_deg 17.42 r_dihedral_angle_3_deg 15.224 r_dihedral_angle_1_deg 7.272 r_angle_refined_deg 1.129 r_angle_other_deg 1.123 r_chiral_restr 0.051 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2065 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 32
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing