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Transthyretin complexed with (E)-4-(2-(naphthalen-1-yl)vinyl)benzene-1,2-diol
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 TTR:SB11 complex 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 45.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.048 α = 90 b = 64.749 β = 90 c = 85.046 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 1.45 43.05 100 0.051 0.054 0.017 0.999 22.1 10.5 42962 19.152
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 1.45 1.47 99.9 1.376 1.444 0.431 0.799 10.7
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 1.45 42.56 40701 2199 99.89 0.1344 0.1328 0.1371 0.1633 0.1671 RANDOM 25.327
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] -0.74 1.56 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.86 r_dihedral_angle_4_deg 14.394 r_dihedral_angle_3_deg 12.782 r_dihedral_angle_1_deg 6.399 r_rigid_bond_restr 1.97 r_angle_refined_deg 1.467 r_angle_other_deg 1.389 r_chiral_restr 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.86 r_dihedral_angle_4_deg 14.394 r_dihedral_angle_3_deg 12.782 r_dihedral_angle_1_deg 6.399 r_rigid_bond_restr 1.97 r_angle_refined_deg 1.467 r_angle_other_deg 1.389 r_chiral_restr 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_gen_planes_other 0.007 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1756 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 47
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction