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Ligand binding domain of human PPAR gamma in complex with amorfrutin 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PRG PDB ENTRY 1PRG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 0.8M TRI-SODIUM CITRATE, 0.1M IMIDAZOLE, PH 8.0
Crystal Properties Matthews coefficient Solvent content 2.6 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.81 α = 90 b = 61.1 β = 102.78 c = 118.22 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 RIGAKU SATURN 944 PLUS 2010-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 27.5 99.5 0.11 15.82 6.7 43633 3.1 42.5
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 2.15 99.8 0.64 3.1 6
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 1PRG 2 27.58 41449 2182 100 0.20672 0.20425 0.2045 0.25385 0.251 RANDOM 44.026
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] -0.18 0.47 2.29 -1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.779 r_dihedral_angle_4_deg 18.668 r_dihedral_angle_3_deg 16.272 r_dihedral_angle_1_deg 5.236 r_scangle_it 3.208 r_scbond_it 1.918 r_mcangle_it 1.267 r_angle_refined_deg 1.243 r_mcbond_it 0.679 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.779 r_dihedral_angle_4_deg 18.668 r_dihedral_angle_3_deg 16.272 r_dihedral_angle_1_deg 5.236 r_scangle_it 3.208 r_scbond_it 1.918 r_mcangle_it 1.267 r_angle_refined_deg 1.243 r_mcbond_it 0.679 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4224 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing