8ALP
Botulinum neurotoxin A6 cell binding domain crystal form II
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 289.15 | 0.1 M magnesium acetate tetrahydrate, 0.1 M MES pH 6.5, 12% w/v of 50% PEG smear medium (4.55% v/v PEG 400, 4.55% v/v PEG 500 MME, 4.55% v/v PEG 600, 4.55% w/v PEG 1000, 4.55% w/v PEG 2000, 4.55% w/v PEG 3350, 4.55% w/v PEG 4000, 4.55% w/v PEG 5000 MME, 4.55% w/v PEG 6000, 4.55% w/v PEG 8000, 4.55% w/v PEG 10000) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.83 | 32.63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 39.554 | α = 90 |
b = 78.938 | β = 90 |
c = 118.55 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 EIGER2 XE 16M | 2021-10-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9795 | Diamond | I04 |
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 | 1.5 | 118.55 | 99.6 | 0.119 | 0.023 | 1 | 12 | 26.3 | 60147 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.5 | 1.53 | 97.5 | 5.68 | 1.125 | 0.33 | 0.7 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6TWO | 1.5 | 65.705 | 60047 | 2990 | 99.432 | 0.251 | 0.2484 | 0.2893 | 37.142 |
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] | |
-0.442 | 1.803 | -1.362 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.242 |
r_dihedral_angle_4_deg | 19.978 |
r_dihedral_angle_3_deg | 15.951 |
r_lrange_it | 8.219 |
r_lrange_other | 8.203 |
r_dihedral_angle_1_deg | 7.584 |
r_scangle_it | 5.947 |
r_scangle_other | 5.946 |
r_mcangle_it | 4.562 |
r_mcangle_other | 4.561 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3127 |
Nucleic Acid Atoms | |
Solvent Atoms | 124 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DIALS | data reduction |
Aimless | data scaling |
PHASER | phasing |