3FZY
Crystal Structure of Pre-cleavage Form of Cysteine Protease Domain from Vibrio cholerae RtxA Toxin
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 295 | The PEGs II Suite, condition 72 mixed 1:1 v/v with 7.3mg/mL protein, 0.3M NaCl, 0.5mM InsP6, 10mM Tris-HCl (pH 7.4), VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 8.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.06 | 40.38 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.055 | α = 90 |
b = 66.373 | β = 90 |
c = 137.958 | 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 | beryllium lenses | 2008-09-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
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 | 1.95 | 25 | 99.4 | 0.076 | 6.7 | 32396 | 32396 | -3 | 33.5 |
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 | 1.95 | 1.98 | 95.3 | 0.448 | 3.1 | 3.9 | 1524 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 3EEB | 1.95 | 23.67 | 29932 | 29932 | 1584 | 99.62 | 0.1713 | 0.1713 | 0.16893 | 0.21616 | RANDOM | 32.053 |
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] | |
2.94 | -3.42 | 0.48 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.739 |
r_dihedral_angle_4_deg | 13.979 |
r_dihedral_angle_3_deg | 11.971 |
r_scangle_it | 4.773 |
r_dihedral_angle_1_deg | 4.556 |
r_scbond_it | 3.237 |
r_mcangle_it | 2.062 |
r_angle_refined_deg | 1.696 |
r_mcbond_it | 1.259 |
r_angle_other_deg | 0.966 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3274 |
Nucleic Acid Atoms | |
Solvent Atoms | 313 |
Heterogen Atoms | 85 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |