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Crystal Structure of PPARgamma LBD bound to full agonist MRL20
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KNU PDB entry 1KNU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 1.4 M sodium citrate, 0.125 M Tris 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.64 53.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.161 α = 90 b = 63.939 β = 103.43 c = 119.187 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 CCD MARMOSAIC 325 mm CCD Mirrors M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.9537 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.2 15 99.2 0.073 0.073 23.1 6.8 32936 57.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 95.7 0.423 0.42 2.9 4.3 3140
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 PDB entry 1KNU 2.2 15 32930 1667 99.19 0.185 0.183 0.1814 0.23 0.2286 RANDOM 21.892
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] -0.48 -0.33 1.25 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.239 r_dihedral_angle_4_deg 19.402 r_dihedral_angle_3_deg 16.005 r_dihedral_angle_1_deg 5.92 r_scangle_it 1.608 r_angle_refined_deg 1.302 r_scbond_it 1.04 r_mcangle_it 0.644 r_mcbond_it 0.384 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.239 r_dihedral_angle_4_deg 19.402 r_dihedral_angle_3_deg 16.005 r_dihedral_angle_1_deg 5.92 r_scangle_it 1.608 r_angle_refined_deg 1.302 r_scbond_it 1.04 r_mcangle_it 0.644 r_mcbond_it 0.384 r_nbtor_refined 0.3 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.185 r_symmetry_hbond_refined 0.171 r_xyhbond_nbd_refined 0.13 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4025 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 76
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction MOLREP phasing