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PPARg bound to inverse agonist H3B-343
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PRG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 296 2+2 uL drops of protein + reservoir consisting of 0.9-1.2 M Na citrate and 100 mM Tris pH 8.0. Protein formulated at 20 mg mL-1 in 20 mM Tris, pH 8.0, 100 mM NaCl, and 1mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.71 54.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.758 α = 90 b = 63.503 β = 101.4 c = 118.333 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 120 IMAGE PLATE MAR scanner 300 mm plate 2017-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D .9786 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.95 50 99.9 0.088 0.098 0.044 8.8 5 14263
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 2.95 3 99.3 0.961 1.09 0.506 0.748 4.6
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 2PRG 2.95 49.51 13274 988 99.41 0.2032 0.1982 0.1992 0.2669 0.2675 RANDOM 81.367
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] -0.09 0.05 -0.11 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.534 r_dihedral_angle_4_deg 22.678 r_dihedral_angle_3_deg 17.6 r_dihedral_angle_1_deg 6.339 r_angle_refined_deg 1.47 r_angle_other_deg 1.03 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.534 r_dihedral_angle_4_deg 22.678 r_dihedral_angle_3_deg 17.6 r_dihedral_angle_1_deg 6.339 r_angle_refined_deg 1.47 r_angle_other_deg 1.03 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4019 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing