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PPARgamma antagonist (MMT-160)- PPARgamma LBD complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VV3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M Tris-HCl pH 7.4, 0.8M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.69 54.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.51 α = 90 b = 61.75 β = 101.93 c = 119.62 γ = 90
Symmetry Space Group C 1 2 1
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 S 2M 2020-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 3 45.83 99.2 0.06 0.074 0.042 0.99 10.8 3 13393
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 3 3.18 99.8 0.242 0.292 0.161 0.939 3.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2VV3 3.2 45.79 10575 527 98.78 0.2179 0.2151 0.2733 0.3015 RANDOM 63.939
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] -5.31 4.54 -1.02 4.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.986 r_dihedral_angle_4_deg 20.236 r_dihedral_angle_3_deg 19.175 r_dihedral_angle_1_deg 6.18 r_angle_refined_deg 2.038 r_chiral_restr 0.123 r_bond_refined_d 0.02 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3928 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction MOSFLM data reduction REFMAC phasing