☰ Navigation Tabs
Crystal structure of PPARgamma in complex with compound (R)-16
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AVI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 33% PEG 3350, 0.1 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.54 51.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.059 α = 90 b = 62.059 β = 90 c = 167.021 γ = 90
Symmetry Space Group P 41 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 PIXEL DECTRIS EIGER X 16M 2020-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99998 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.62 43.88 99.8 0.058 0.067 0.025 0.999 15.3 7.1 10478
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.62 2.76 100 0.932 1.07 0.383 0.742 7.6
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 6avi 2.62 43.88 9931 494 99.62 0.2083 0.206 0.2106 0.2536 0.2549 RANDOM 95.116
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] -0.32 -0.32 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.44 r_dihedral_angle_4_deg 16.212 r_dihedral_angle_3_deg 15.524 r_dihedral_angle_1_deg 7.42 r_angle_refined_deg 1.177 r_angle_other_deg 1.162 r_chiral_restr 0.057 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.44 r_dihedral_angle_4_deg 16.212 r_dihedral_angle_3_deg 15.524 r_dihedral_angle_1_deg 7.42 r_angle_refined_deg 1.177 r_angle_other_deg 1.162 r_chiral_restr 0.057 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2065 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 32
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing