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Structure of the amyloid-forming peptide LYIQWL from Tc5b, grown from 10% ethanol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other crystal structure of LYIQWL grown from acetonitrile/water
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION, RECRYSTALLIZATION 293 Peptide was dissolved in 10% ethanol at 0.5 mg/ml concentration, then incubated at 293K overnight.
Crystal Properties Matthews coefficient Solvent content 1.54 20.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 11.719 α = 90 b = 23.467 β = 90.04 c = 18.762 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 2022-01-26 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 1.35 18.76 98.13 0.168 0.998 7 4.93 2253 5.6
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 1.35 1.4 0.745 0.756 2.2
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 crystal structure of LYIQWL grown from acetonitrile/water 1.35 18.76 1.38 2244 221 97.74 0.1177 0.1142 0.1144 0.1522 0.1515 5.95
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 14.9744 f_angle_d 1.4097 f_chiral_restr 0.1112 f_bond_d 0.0128 f_plane_restr 0.0086
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 120 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 13
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction CrysalisPro data scaling PHASER phasing