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Neutron structure of human transthyretin (TTR) T119M mutant at room temperature to 1.85A resolution
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CM1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 1.9M sodium malonate pD5.9, 40mg/ml protein
Crystal Properties Matthews coefficient Solvent content 2.19 43.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.71 α = 90 b = 86.32 β = 90 c = 65.338 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 298 IMAGE PLATE BIODIFF 2016-09-08 M SINGLE WAVELENGTH 2 1 x-ray 293 PIXEL DECTRIS PILATUS 6M-F 2016-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 NUCLEAR REACTOR FRM II BEAMLINE BIODIFF 2.67 FRM II BIODIFF 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 1.85 43.61 90.6 0.164 0.136 3.7 2 19760 2 1.85 33.49 97.3 0.047 0.025 27.1 4.4 19760
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 1.85 1.9 0.526 0.499 1.2 1.7 2 1.85 1.95 0.062 0.033 16.7 4.3
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 1.853 43.16 1.99 20896 2091 96.34 0.1677 0.1648 0.1666 0.1941 0.1963 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 1.85 33.485 19744 1975 90.69 0.2173 0.2132 0.2536
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 13.337 f_dihedral_angle_d 13.337 f_angle_d 1.548 f_angle_d 1.548 f_chiral_restr 0.082 f_chiral_restr 0.082 f_bond_d 0.014 f_bond_d 0.014 f_plane_restr 0.009 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1794 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction XDS data reduction HKL-2000 data scaling SCALA data scaling Coot model building REFMAC phasing