5CXL
CRYSTAL STRUCTURE OF RTX DOMAIN BLOCK V OF ADENYLATE CYCLASE TOXIN FROM BORDETELLA PERTUSSIS
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5CVW | PDB ENTRY 5CVW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 291.15 | BUFFER COMPOSITION: 5 mM TRIS-HCL PH=7.4, 150 mM NaCl, 10 mM CaCl2. PRECIPITANT COMPOSITION: 0.2 M MAGNESIUM NITRATE, 20% V/V PEG 3350, |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.08 | 40.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.225 | α = 90 |
b = 52.225 | β = 90 |
c = 195.952 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
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 | 90 | CCD | MARMOSAIC 225 mm CCD | 2 MIRRORS | 2012-07-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.918410 | BESSY | 14.1 |
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 | 1.45 | 50 | 99.9 | 0.056 | 22.11 | 8.55 | 46709 | -3 |
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 | 1.45 | 1.54 | 99.8 | 0.787 | 2.55 |
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 5CVW | 1.45 | 32.15 | 46709 | 2458 | 99.9 | 0.151 | 0.148 | 0.207 | RANDOM | 22.57 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.037 |
r_sphericity_free | 29.623 |
r_sphericity_bonded | 19.239 |
r_dihedral_angle_4_deg | 19.128 |
r_dihedral_angle_3_deg | 14.331 |
r_rigid_bond_restr | 6.18 |
r_dihedral_angle_1_deg | 6.163 |
r_angle_refined_deg | 1.92 |
r_chiral_restr | 0.148 |
r_bond_refined_d | 0.019 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2172 |
Nucleic Acid Atoms | |
Solvent Atoms | 221 |
Heterogen Atoms | 24 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
PHASER | phasing |
REFMAC | refinement |
XDS | data scaling |