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Crystal structure of PPARgammaLBD complexed with the agonist magnolol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ADX PDB ENTRY 3ADX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 4 M sodium formate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.7 54.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.04 α = 90 b = 66.04 β = 90 c = 155.26 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 CCD MARMOSAIC 225 mm CCD 2011-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U SSRF BL17U
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 60.77 94.2 0.053 0.053 51.8 5.9 23970 22532 2 2
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 2.07 90.7 0.398 0.398 7.2 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3ADX 2 60.77 22532 22532 1102 89.76 0.26007 0.25832 0.2575 0.29304 0.2774 RANDOM 41.02
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] -0.12 -0.12 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.544 r_dihedral_angle_3_deg 14.896 r_dihedral_angle_4_deg 10.905 r_dihedral_angle_1_deg 4.103 r_angle_refined_deg 0.958 r_scangle_it 0.933 r_scbond_it 0.66 r_mcangle_it 0.644 r_mcbond_it 0.384 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.544 r_dihedral_angle_3_deg 14.896 r_dihedral_angle_4_deg 10.905 r_dihedral_angle_1_deg 4.103 r_angle_refined_deg 0.958 r_scangle_it 0.933 r_scbond_it 0.66 r_mcangle_it 0.644 r_mcbond_it 0.384 r_nbtor_refined 0.295 r_nbd_refined 0.168 r_symmetry_vdw_refined 0.148 r_symmetry_hbond_refined 0.096 r_xyhbond_nbd_refined 0.095 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2046 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 40
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling