☰ Navigation Tabs
Structure of the amyloid-forming peptide YLAAVL from human PACAP, polymorph B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION, RECRYSTALLIZATION 310 the peptide was dissolved at approximately 1 mg/ml in 0.2 M acetate buffer containing 30% (v/v) acetonitrile and incubated at 310 K
Crystal Properties Matthews coefficient Solvent content 1.49 17.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 20.035 α = 90 b = 18.703 β = 92.69 c = 20.616 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 2024-06-12 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 1.3 14.7 98.94 0.076 0.998 7.1 4.22 3831 6.26
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 1.3 1.35 98.44 0.416 0.958
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 1.3 14.7 1.39 3771 382 97.44 0.2199 0.2183 0.2187 0.2335 0.2332 8.57
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 11.7711 f_angle_d 2.3194 f_chiral_restr 0.1256 f_bond_d 0.0236 f_plane_restr 0.0164
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 184 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction CrysalisPro data scaling SHELXT phasing