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PPARdelta complexed with an anthranilic acid partial agonist
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GWX PDB entry 3GWX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 298 100mM potassium iodide, PEG3500, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.91 57.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.886 α = 90 b = 94.324 β = 98.3 c = 97.066 γ = 90
Symmetry Space Group P 1 21 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 MAR CCD 165 mm 2004-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.9 96.22 97.16 0.073 17 3.4 14657 14657 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.975 76 0.25 2 2 852
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3GWX 2.9 24.01 2 14657 14657 786 97.16 0.21852 0.21708 0.2175 0.24445 RANDOM 66.22
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] 2.63 0.51 3.55 -6.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.917 r_dihedral_angle_3_deg 15.243 r_dihedral_angle_4_deg 13.452 r_dihedral_angle_1_deg 4.51 r_scangle_it 1.173 r_angle_refined_deg 1.048 r_scbond_it 0.672 r_mcangle_it 0.414 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.259
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.917 r_dihedral_angle_3_deg 15.243 r_dihedral_angle_4_deg 13.452 r_dihedral_angle_1_deg 4.51 r_scangle_it 1.173 r_angle_refined_deg 1.048 r_scbond_it 0.672 r_mcangle_it 0.414 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.259 r_mcbond_it 0.229 r_nbd_refined 0.197 r_symmetry_hbond_refined 0.162 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 4064 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement