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Structure of the amyloid-forming peptide Ac-YLESLM-OH from human PHM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION, RECRYSTALLIZATION 310 the peptide was dissolved at 1 mg/ml in water containing 30% (v/v) acetonitrile (pH 4) and incubated at 310 K
Crystal Properties Matthews coefficient Solvent content 1.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.29 α = 90 b = 9.51 β = 118.571 c = 19.01 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 310 PIXEL RIGAKU HyPix-6000HE 2024-06-24 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 1.246 13.164 94.1 0.073 0.998 14.4 3.4 1210 5.66
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 1.246 1.371 0.316 0.837 3.1
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 1.25 13.16 1.42 1207 66 95.26 0.0915 0.0911 0.0911 0.096 0.096 4.84
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 35.6916 f_angle_d 1.2011 f_chiral_restr 0.0893 f_bond_d 0.0092 f_plane_restr 0.0047
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 52 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 3
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction XSCALE data scaling SHELXT phasing