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Structure of the amyloid-forming peptide YLESLM from human PHM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION, RECRYSTALLIZATION 310 the peptide was dissolved in 0.2 M acetate buffer (pH 4.67) at a concentration of 5 mg/ml and incubated at 310 K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 4.833 α = 90 b = 18.483 β = 90 c = 43.363 γ = 90
Symmetry Space Group P 21 21 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 RIGAKU HyPix-6000HE 2024-01-24 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 1.05 21.69 99.95 0.219 0.994 5.4 4.49 2136 5.36
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 1.05 1.09 1.351 0.605 1.8
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 AB INITIO PHASING FREE R-VALUE 1.05 21.68 1.34 2118 208 99.11 0.1909 0.1887 0.188 0.2104 0.2084 7.21
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 20.2406 f_angle_d 1.5275 f_chiral_restr 0.0779 f_bond_d 0.0184 f_plane_restr 0.0055
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 52 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction CrysalisPro data scaling SHELXT phasing