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Structure of the amyloid-forming peptide LYIQWL from Tc5b, grown from 30% acetonitrile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other ideal 5 residue beta strand form the software Fragon
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION, RECRYSTALLIZATION 310 Peptide was dissolved in 30% acetonitrile at 0.2 mg/ml concentration and incubated at 310K
Crystal Properties Matthews coefficient Solvent content 1.52 19.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 11.744 α = 90 b = 23.164 β = 90.23 c = 18.715 γ = 90
Symmetry Space Group P 1 21 1
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 RIGAKU HyPix-6000HE 2021-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU PhotonJet-R 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.25 14.56 99.33 0.139 0.998 9.2 6.6 2829 5.88
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.29 97.26 0.468 0.777 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 ideal 5 residue beta strand form the software Fragon 1.25 14.56 1.41 2817 275 98.91 0.1017 0.0979 0.0979 0.1374 0.1381 5.98
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 15.3249 f_angle_d 1.0843 f_chiral_restr 0.1014 f_bond_d 0.0115 f_plane_restr 0.0092
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 120 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 13
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction CrysalisPro data scaling Fragon phasing