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Human PPARgamma ligand binding domain complexed with Rosiglitazone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GTO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 296 2.2 M sodium malonate (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 2.77 55.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.809 α = 90 b = 53.133 β = 90 c = 54.57 γ = 90
Symmetry Space Group P 21 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 ADSC QUANTUM 315r 2015-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97960 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 99.9 53.4 9.9
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 5GTO 2 30 25141 1317 99.87 0.20287 0.20132 0.2099 0.23338 0.2368 RANDOM 44.458
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] -0.9 1.13 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.001 r_dihedral_angle_4_deg 21.224 r_dihedral_angle_3_deg 13.649 r_long_range_B_refined 8.097 r_long_range_B_other 8.095 r_scangle_other 6.243 r_dihedral_angle_1_deg 5.545 r_mcangle_it 4.553 r_mcangle_other 4.553 r_scbond_it 3.952
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.001 r_dihedral_angle_4_deg 21.224 r_dihedral_angle_3_deg 13.649 r_long_range_B_refined 8.097 r_long_range_B_other 8.095 r_scangle_other 6.243 r_dihedral_angle_1_deg 5.545 r_mcangle_it 4.553 r_mcangle_other 4.553 r_scbond_it 3.952 r_scbond_other 3.95 r_angle_other_deg 3.51 r_mcbond_it 3.167 r_mcbond_other 3.166 r_angle_refined_deg 1.486 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_other 0.008 r_gen_planes_refined 0.007 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2206 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing