4QO6
Structural studies of CdsD, a structural protein of the Type III secretion system (TTSS) of Chlamydia trachomatis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 295 | 50 mM MES; pH 6.0 - 3 % PEG4000 - 15 % 2-propanol - 50 mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.01 | 59.08 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 106.6 | α = 90 |
b = 23.91 | β = 104.95 |
c = 118.65 | 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 | PIXEL | DECTRIS PILATUS 2M | 2013-02-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.92 | Diamond | I04-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.26 | 28.66 | 97.6 | 14312 | 13969 | 2 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.26 | 2.39 | 92.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | SAD | THROUGHOUT | 2.26 | 28.66 | 2 | 14312 | 13267 | 699 | 98.03 | 0.19696 | 0.19462 | 0.24133 | RANDOM | 38.091 |
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] | |
3.5 | -0.68 | -1.26 | -1.65 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.569 |
r_dihedral_angle_4_deg | 17.013 |
r_dihedral_angle_3_deg | 15.524 |
r_long_range_B_refined | 8.504 |
r_long_range_B_other | 8.501 |
r_dihedral_angle_1_deg | 6.966 |
r_scangle_other | 6.098 |
r_mcangle_it | 4.472 |
r_mcangle_other | 4.47 |
r_scbond_it | 3.768 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1655 |
Nucleic Acid Atoms | |
Solvent Atoms | 82 |
Heterogen Atoms | 15 |
Software
Software | |
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Software Name | Purpose |
GDA | data collection |
PHENIX | model building |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
PHENIX | phasing |