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Crystal structure of human transthyretin (TTR) with pryazole-based stabilizer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HJ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.2M CaCl2, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.15 42.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.948 α = 90.03 b = 65.187 β = 89.98 c = 84.665 γ = 89.99
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 180 PIXEL DECTRIS PILATUS 6M 2025-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 11C 0.97942 PAL/PLS 11C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.58 50 88 0.989 26.5 3.8 113158 8.92
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.61 80.8 0.924 5.7 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.58 42.33 1.98 113089 2014 88.24 0.1726 0.1724 0.1725 0.1797 0.18 14.2
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.9791 f_angle_d 0.9211 f_chiral_restr 0.0642 f_plane_restr 0.0084 f_bond_d 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7168 Nucleic Acid Atoms Solvent Atoms 709 Heterogen Atoms 72
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing