3KI7
Catalytic fragment of Cholix toxin from Vibrio Cholerae in complex with inhibitor GP-I
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 298 | 5% PEG-8000, 0.02 M KH2PO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.25 | 45.34 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 35.467 | α = 90 |
b = 64.898 | β = 90 |
c = 91.756 | 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 | CCD | MARMOSAIC 225 mm CCD | 2008-01-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | 0.97934 | CLSI | 08ID-1 |
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 | 1.32 | 50 | 91 | 0.121 | 5.8 | 6.7 | 46297 | -3 | 8.4 |
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) | |||||||||||
1.32 | 1.37 | 87.4 | 0.282 | 5.6 | 5.2 | 4380 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2Q6M | 1.32 | 18.73 | 46202 | 2338 | 92.01 | 0.152 | 0.15 | 0.174 | RANDOM | 9.887 |
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] | |
-0.02 | 0.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.807 |
r_dihedral_angle_3_deg | 12.158 |
r_dihedral_angle_4_deg | 11.264 |
r_dihedral_angle_1_deg | 5.972 |
r_sphericity_free | 4.282 |
r_scangle_it | 2.919 |
r_sphericity_bonded | 2.532 |
r_scbond_it | 2.19 |
r_mcangle_it | 1.541 |
r_angle_refined_deg | 1.342 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1554 |
Nucleic Acid Atoms | |
Solvent Atoms | 395 |
Heterogen Atoms | 28 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Macromolecular | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |