6ES1
Crystal structure of the binding domain from botulinum neurotoxin A2 bound to extracellular domain of human receptor SV2C
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 293 | 0.160 mM HcA2 (8.27 mg/mL), 0.160 mM SV2CL4 (2.24 mg/mL), 2 mM Sialylated Thomsen-Friedenreich carbohydrate antigen (Sialyl-T). Reservoir solution: 200 mM CaCl2, 100 mM MES pH 6.0, 20 % PEG 6000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.24 | 45 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 100.714 | α = 90 |
b = 122.108 | β = 90 |
c = 47.657 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 PILATUS 6M | 2015-07-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.919908 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2 | 47.66 | 99.8 | 0.242 | 0.996 | 9.4 | 13.2 | 40692 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2 | 2.05 | 97.7 | 1.237 | 0.481 | 2.2 | 13.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4JRA chain C; 3BTA | 2 | 47.66 | 38627 | 2010 | 99.81 | 0.18387 | 0.18139 | 0.22967 | RANDOM | 27.539 |
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] | |
1.86 | -0.7 | -1.16 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.602 |
r_dihedral_angle_3_deg | 14.658 |
r_dihedral_angle_4_deg | 14.271 |
r_dihedral_angle_1_deg | 6.947 |
r_long_range_B_refined | 4.758 |
r_long_range_B_other | 4.758 |
r_mcangle_it | 1.666 |
r_mcangle_other | 1.665 |
r_angle_refined_deg | 1.663 |
r_scangle_other | 1.633 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4234 |
Nucleic Acid Atoms | |
Solvent Atoms | 359 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |