7ATR
The Crystal Structure of YejA - an ABC Peptide Transporter Receptor
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 291 | Protein: 20 mg.ml-1 in 20 mM Tris-HCl, 50 mM NaCl, pH 8.0 Reservoir solution: 2% w/v polyethylene glycol 20,000, 0.1 M 2-(N-morpholino)ethanesulfonic acid, pH 6.5 Drops: 300 nl (150 nl protein solution + 150 nl reservoir solution) Reservoir: 100 microlitres |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.57 | 52.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 91.44 | α = 90 |
b = 105.267 | β = 90 |
c = 145.387 | γ = 90 |
Symmetry | |
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Space Group | I 2 2 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 | 100 | PIXEL | DECTRIS PILATUS3 S 6M | 2017-05-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.92819 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.55 | 85.264 | 99.6 | 0.07 | 0.08 | 0.038 | 0.997 | 14.1 | 8.4 | 101011 | 15.46 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.55 | 1.58 | 0.668 | 0.756 | 0.353 | 0.904 | 2.4 | 8.5 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 4ONY | 1.55 | 85.264 | 101009 | 4874 | 99.528 | 0.171 | 0.1701 | 0.1846 | 20.793 |
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] | |
1.846 | -0.539 | -1.307 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.24 |
r_dihedral_angle_4_deg | 17.618 |
r_dihedral_angle_3_deg | 12.952 |
r_dihedral_angle_1_deg | 6.791 |
r_lrange_it | 5.839 |
r_lrange_other | 5.749 |
r_scangle_it | 4.862 |
r_scangle_other | 4.862 |
r_scbond_it | 3.283 |
r_scbond_other | 3.282 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4841 |
Nucleic Acid Atoms | |
Solvent Atoms | 408 |
Heterogen Atoms | 18 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data processing |
Aimless | data reduction |
Aimless | data scaling |
MOLREP | phasing |