4QX1
Cry3A Toxin structure obtained by Serial Femtosecond Crystallography from in vivo grown crystals isolated from Bacillus thuringiensis and data processed with the CrystFEL software suite
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1DLC | PDB ENTRY 1DLC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | IN VIVO CRYSTALLIZATION | 303 | Cry3A crystallized within the bacterial cell, IN VIVO CRYSTALLIZATION, temperature 303K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.14 | 60.88 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 117.1 | α = 90 |
b = 135.4 | β = 90 |
c = 105.6 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | 298 | PIXEL | Cornell-SLAC Pixel Array Detector (CSPAD) | 2013-03-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE CXI | 1.456 | SLAC LCLS | CXI |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.8 | 88.6 | 100 | 0.159 | 9.5 | 1128 | 21038 | 21038 | 80.64 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.8 | 2.9 | 100 | 0.412 | 1.6 | 691.5 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | FOURIER SYNTHESIS | THROUGHOUT | PDB ENTRY 1DLC | 2.8 | 44.29 | 21030 | 1038 | 100 | 0.179 | 0.178 | 0.1973 | RANDOM | 75.68 |
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] | |
13.0141 | 7.6603 | -20.6744 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 18.75 |
t_omega_torsion | 2.6 |
t_angle_deg | 1.02 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4659 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
BUSTER-TNT | refinement |
PDB_EXTRACT | data extraction |
CrystFEL | data reduction |
CrystFEL | data scaling |
BUSTER | refinement |