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Structure of the amyloid-forming peptide YLNSIL from human VIP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other ideal polyalanine beta strand
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION, RECRYSTALLIZATION 310 the peptide was dissolved at a concentration of 0.4 mg/ml in 30% (v/v) methanol with 0.2 M acetate buffer (pH 3.77) and incubated at 310 K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 4.92 α = 90 b = 16.96 β = 90 c = 45.54 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 DECTRIS EIGER2 XE 16M 2023-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97628 Diamond I03
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 1.15 22.77 89.3 0.114 0.998 12.4 10.8 1450 7.86
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 1.15 1.17 0.592 0.801
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 MOLECULAR REPLACEMENT FREE R-VALUE 1.15 22.77 1.37 1447 145 89.05 0.0758 0.0735 0.0737 0.1002 0.1003 6.93
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 14.7786 f_angle_d 1.5924 f_chiral_restr 0.1148 f_plane_restr 0.0212 f_bond_d 0.0137
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 51 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction XSCALE data scaling PHASER phasing