☰ Navigation Tabs
Ligand binding domain of PPAR delta receptor in complex with a partial agonist
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GWX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.49 50.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.577 α = 90 b = 65.603 β = 124.05 c = 101.149 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 95 CCD ADSC QUANTUM 4 2006-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 1.00 ALS 5.0.3
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 2.7 53.73 95.7 0.099 6.3 2.53 16233
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 2.7 2.8 98.6 0.373 2.1 2.47 1645
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 2GWX 2.7 53.73 16225 826 95.6 0.229 0.225 0.2307 0.305 0.3016 RANDOM 41.635
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] 2.2 -0.67 0.16 -3.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.517 r_dihedral_angle_3_deg 19.938 r_dihedral_angle_4_deg 14.516 r_dihedral_angle_1_deg 6.165 r_scangle_it 2.476 r_angle_refined_deg 1.625 r_scbond_it 1.532 r_mcangle_it 1.436 r_mcbond_it 0.846 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.517 r_dihedral_angle_3_deg 19.938 r_dihedral_angle_4_deg 14.516 r_dihedral_angle_1_deg 6.165 r_scangle_it 2.476 r_angle_refined_deg 1.625 r_scbond_it 1.532 r_mcangle_it 1.436 r_mcbond_it 0.846 r_nbtor_refined 0.314 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.149 r_symmetry_vdw_refined 0.146 r_symmetry_hbond_refined 0.108 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3792 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 84
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction d*TREK data reduction PHASES phasing