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Neutron structure of human transthyretin (TTR) S52P mutant in complex with tafamidis at room temperature to 2A resolution (quasi-Laue)
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CLX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2.3M sodium malonate pD 5.9
Crystal Properties Matthews coefficient Solvent content 2.19 43.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.901 α = 90 b = 85.703 β = 90 c = 65.54 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 neutron 293 IMAGE PLATE LADI III 2017-03-01 L LAUE 2 1 x-ray 293 PIXEL DECTRIS PILATUS 6M-F 2017-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 NUCLEAR REACTOR ILL BEAMLINE LADI III 2.7-3.6 ILL LADI III 2 SYNCHROTRON ESRF BEAMLINE ID30B 0.9763 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 43.9 71.9 0.121 0.07 6 2.6 17225 23.28 2 2 35.85 98.7 0.041 0.021 31 4.6 12103 19.34
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 0.208 0.151 4 2.2 2 2 2.11 0.046 0.023 23.3 4.7
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2 42.852 2.06 17192 1718 99.24 0.1612 0.1574 0.1592 0.1947 0.1962 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2 35.866 12097 1211 69.83 0.2363 0.2313 0.2801
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 14.635 f_dihedral_angle_d 14.635 f_angle_d 1.975 f_angle_d 1.975 f_chiral_restr 0.088 f_chiral_restr 0.088 f_bond_d 0.017 f_bond_d 0.017 f_plane_restr 0.01 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1794 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement LAUEGEN data reduction XDS data reduction LSCALE data scaling SCALA data scaling REFMAC phasing Coot model building