3EB7
Crystal Structure of Insecticidal Delta-Endotoxin Cry8Ea1 from Bacillus Thuringiensis at 2.2 Angstroms Resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1CIY | PDB ENTRY 1CIY |
Crystallization
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.53 | 51.41 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 407.282 | α = 90 |
b = 47.956 | β = 91.12 |
c = 103.121 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | CCD | ADSC QUANTUM 315 | mirrors | 2006-11-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 1 | Photon Factory | BL-5A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.2 | 204.1 | 97.4 | 0.137 | 0.137 | 12.3 | 4.5 | 101555 | 98915 | 1 | 1 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.2 | 2.28 | 84.1 | 0.46 | 0.46 | 2.07 | 2.8 | 10105 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B |
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1CIY | 2.3 | 43.2 | 1 | 1 | 80780 | 79964 | 8885 | 98.99 | 0.17103 | 0.16913 | 0.16235 | 0.16 | 0.23009 | 0.23 | RANDOM | 26.555 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
-1.43 | 0.74 | 0.28 | 1.18 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.91 |
r_dihedral_angle_4_deg | 19.997 |
r_dihedral_angle_3_deg | 18.285 |
r_dihedral_angle_1_deg | 6.716 |
r_scangle_it | 3.659 |
r_scbond_it | 2.399 |
r_angle_refined_deg | 1.575 |
r_mcangle_it | 1.454 |
r_mcbond_it | 0.856 |
r_nbtor_refined | 0.309 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14049 |
Nucleic Acid Atoms | |
Solvent Atoms | 1101 |
Heterogen Atoms | 77 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
CNS | refinement |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CNS | phasing |