6F0P
Botulinum neurotoxin A4 Hc domain
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 289 | 10 mM Spermine tetrahydrochloride, 10 mM Spermidine trihydrochloride, 10 mM 1,4-Diaminobutane dihydrochloride, 10 mM D-L-Ornithine monohydrochloride, 0.1 M MOPSO/bis-tris pH 6.5, 15%(w/v) PEG 3K, 20%(v/v) 1,2,4-butanetriol, 1%(w/v) NDSB 256 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.56 | 51.86 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 115.888 | α = 90 |
b = 115.888 | β = 90 |
c = 115.888 | γ = 90 |
Symmetry | |
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Space Group | P 21 3 |
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 PILATUS3 6M | 2017-04-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9763 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim 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 | 1.34 | 81.95 | 100 | 0.091 | 0.02 | 0.999 | 17.5 | 21.7 | 116165 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.34 | 1.36 | 100 | 2.306 | 0.74 | 0.421 | 1.1 | 10.5 |
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 | 2vua | 1.34 | 81.95 | 113786 | 2017 | 99.98 | 0.14425 | 0.14401 | 0.15829 | RANDOM | 20.807 |
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 | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.928 |
r_sphericity_free | 22.325 |
r_dihedral_angle_4_deg | 16.119 |
r_sphericity_bonded | 12.905 |
r_dihedral_angle_3_deg | 12.675 |
r_dihedral_angle_1_deg | 6.974 |
r_long_range_B_refined | 5.381 |
r_long_range_B_other | 5.38 |
r_scangle_other | 4.639 |
r_mcangle_other | 4.012 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3423 |
Nucleic Acid Atoms | |
Solvent Atoms | 309 |
Heterogen Atoms | 49 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DIALS | data reduction |
Aimless | data scaling |
PHASER | phasing |