7P1P
Crystal structure of human acetylcholinesterase in complex with (E)-3-hydroxy-6-(3-(4-(4-(((2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl)oxy)butyl)-1H-1,2,3-triazol-1-yl)propyl)picolinaldehyde oxime
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4EY4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 1.5 M LiSO4, 100 mM HEPES, 60 mM MgSO4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
6.38 | 80.71 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 211.863 | α = 90 |
b = 211.863 | β = 90 |
c = 116.269 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 | DECTRIS EIGER X 9M | 2018-08-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | 0.8731 | ESRF | ID23-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 3.03 | 91.74 | 99.86 | 0.108 | 0.1161 | 0.999 | 13.06 | 7.4 | 57768 | 78.77 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 3.03 | 3.138 | 0.933 |
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 | 4EY4 | 3.03 | 91.74 | 1.39 | 57768 | 2843 | 99.86 | 0.1923 | 0.1903 | 0.2216 | 88 |
Temperature Factor Modeling | ||||||
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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 | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 9.6006 |
f_angle_d | 1.2133 |
f_chiral_restr | 0.063 |
f_plane_restr | 0.0127 |
f_bond_d | 0.0098 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8315 |
Nucleic Acid Atoms | |
Solvent Atoms | 201 |
Heterogen Atoms | 268 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |