9DSY
Crystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite ATP-independent Periplasmic Transporter Family from Pseudomonas aeruginosa PAO1 in Complex with Succinic Acid
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.3 | 292 | Protein: 7.0 mg/ml, 0.5M Sodium chloride, 0.02M Tris-HCl (pH 8.0), 2mM Succinic acid; Screen: Classics II (H9), 0.05M Zing acetate, 20% (w/v) PEG 3350; Cryo: Reservoir. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.97 | 37.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 34.585 | α = 78.78 |
b = 44.495 | β = 84.22 |
c = 47.239 | γ = 75.83 |
Symmetry | |
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Space Group | P 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 | CCD | MARMOSAIC 300 mm CCD | 2022-04-08 | 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) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.35 | 30 | 95.4 | 0.103 | 0.103 | 0.121 | 0.063 | 0.987 | 13.4 | 3.7 | 55717 | -3 | 13.7 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.35 | 1.37 | 92.9 | 0.894 | 0.559 | 2 | 4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.35 | 29.85 | 52942 | 2775 | 95.22 | 0.17365 | 0.17282 | 0.18922 | RANDOM | 20.752 |
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] | |
0.15 | 0.02 | -0.73 | 0.12 | 0.66 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 8.356 |
r_long_range_B_refined | 5.595 |
r_long_range_B_other | 5.52 |
r_dihedral_angle_1_deg | 4.31 |
r_scangle_other | 3.484 |
r_dihedral_angle_2_deg | 2.436 |
r_scbond_it | 2.224 |
r_scbond_other | 2.224 |
r_mcangle_it | 1.58 |
r_mcangle_other | 1.579 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2411 |
Nucleic Acid Atoms | |
Solvent Atoms | 261 |
Heterogen Atoms | 13 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
HKL-3000 | phasing |