8ANH
Structure of the amyloid-forming peptide LYIQWL from Tc5b, grown from 30% acetonitrile
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | EVAPORATION, RECRYSTALLIZATION | 310 | Peptide was dissolved in 30% acetonitrile at 0.2 mg/ml concentration and incubated at 310K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.52 | 19.31 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 11.744 | α = 90 |
b = 23.164 | β = 90.23 |
c = 18.715 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | 2021-09-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU PhotonJet-R | 1.54184 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.25 | 14.56 | 99.33 | 0.139 | 0.998 | 9.2 | 6.6 | 2829 | 5.88 |
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 | 1.25 | 1.29 | 97.26 | 0.468 | 0.777 | 3.1 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | ideal 5 residue beta strand form the software Fragon | 1.25 | 14.56 | 1.41 | 2817 | 275 | 98.91 | 0.1017 | 0.0979 | 0.1374 | 5.98 |
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 | 15.3249 |
f_angle_d | 1.0843 |
f_chiral_restr | 0.1014 |
f_bond_d | 0.0115 |
f_plane_restr | 0.0092 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 120 |
Nucleic Acid Atoms | |
Solvent Atoms | 2 |
Heterogen Atoms | 13 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
CrysalisPro | data reduction |
CrysalisPro | data scaling |
Fragon | phasing |