6SMS
Vegetative Insecticidal Protein 1 (Vip1Ac1) from Bacillus thuringiensis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 293 | 0.2 M MgCl2, 0.1 M MES, 20% w/v PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.79 | 55.87 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 105.17 | α = 90 |
b = 176.24 | β = 90 |
c = 48.78 | 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 | 2017-01-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
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) | Rrim I (All) | 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 | 1.47 | 51.29 | 100 | 0.054 | 0.058 | 0.022 | 0.999 | 16 | 7.3 | 154836 | 19.5 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.47 | 1.51 | 100 | 1.642 | 1.772 | 0.656 | 0.605 | 1.1 | 7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.47 | 51.29 | 147014 | 7752 | 99.94 | 0.1583 | 0.1562 | 0.1977 | RANDOM | 26.875 |
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] | |
0.43 | 0.35 | -0.79 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.407 |
r_dihedral_angle_4_deg | 17.946 |
r_dihedral_angle_3_deg | 14.364 |
r_dihedral_angle_1_deg | 6.953 |
r_rigid_bond_restr | 4.455 |
r_angle_refined_deg | 1.707 |
r_angle_other_deg | 1.493 |
r_chiral_restr | 0.088 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5714 |
Nucleic Acid Atoms | |
Solvent Atoms | 860 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
SHELX | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |