2H09
Crystal structure of diphtheria toxin repressor like protein from E. coli
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.2 | 298 | PEG 300, Phosphate citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.96 | 37.22 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 75.76 | α = 90 |
b = 75.76 | β = 90 |
c = 41.8 | γ = 120 |
Symmetry | |
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Space Group | P 32 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 | 298 | CCD | ADSC QUANTUM 4 | Silicon II channel | 2006-03-30 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | CCD | ADSC QUANTUM 4 | 2006-03-10 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL26B1 | 1.0000 | SPring-8 | BL26B1 |
2 | SYNCHROTRON | SPRING-8 BEAMLINE BL26B1 | 0.9789, 0.9793, 0.9640 | SPring-8 | BL26B1 |
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 | 2.1 | 50 | 99.4 | 0.0062 | 9.5 | 8314 | 8314 | 1 | 1 | 25.9 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
2.1 | 2.18 | 95.7 | 0.329 | 5.8 | 782 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | MAD | THROUGHOUT | 2.1 | 19.92 | 8314 | 8265 | 678 | 99.5 | 0.238 | 0.238 | 0.258 | RANDOM | 49.6 |
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] | |
9.39 | 5.48 | 9.39 | -18.78 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 21.8 |
c_scangle_it | 4.34 |
c_scbond_it | 2.99 |
c_mcangle_it | 2.38 |
c_mcbond_it | 1.52 |
c_angle_deg | 1.1 |
c_improper_angle_d | 0.73 |
c_bond_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1023 |
Nucleic Acid Atoms | |
Solvent Atoms | 78 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
ADSC | data collection |
CCP4 | data scaling |
SOLVE | phasing |