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Complex of Transthyretin with resveratrol exhibits multiple binding modes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other In house model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 protein at 5.2mg/ml in 10mM sodium phosphate pH7.6 and 100mM potassium chloride was mixed 1:1 with
1.3-1.6M sodium citrate and 3.5% glycerol.
Crystal Properties Matthews coefficient Solvent content 2.26 45.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.068 α = 90 b = 64.304 β = 90 c = 85.293 γ = 90
Symmetry Space Group P 21 2 21
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 EIGER2 X 16M 2018-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.97993 MAX IV BioMAX
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 1.35 43.07 97.9 0.041 0.044 0.017 0.999 18.9 6.7 51539 17.189
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 1.35 1.37 95.3 1.174 1.268 0.476 0.672 6.9
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 In house model 1.35 38.47 48927 2594 97.51 0.1397 0.1378 0.1393 0.1749 0.1778 RANDOM 22.849
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] 1.44 1.52 -2.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.954 r_dihedral_angle_4_deg 17.162 r_dihedral_angle_3_deg 11.961 r_dihedral_angle_1_deg 6.494 r_rigid_bond_restr 2.377 r_angle_refined_deg 1.575 r_angle_other_deg 1.428 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.954 r_dihedral_angle_4_deg 17.162 r_dihedral_angle_3_deg 11.961 r_dihedral_angle_1_deg 6.494 r_rigid_bond_restr 2.377 r_angle_refined_deg 1.575 r_angle_other_deg 1.428 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.009 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1751 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 81
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction