6RXB
Crystal structure of TetR-Q116A from Acinetobacter baumannii AYE in complex with minocycline
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6RX9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 5.5 | 291 | 0.1M Sodium cacodylate, pH5.5, 11% PEG Smear Broad, 3% Tacsimate, pH7.0, and 10% Ethylene glycol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 46.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.543 | α = 90 |
b = 64.227 | β = 90 |
c = 220.954 | 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 | PIXEL | DECTRIS EIGER X 9M | 2018-04-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 2 | 0.979 | SOLEIL | PROXIMA 2 |
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 | 2.25 | 48.41 | 100 | 0.256 | 0.267 | 0.072 | 0.991 | 6 | 13.7 | 43315 |
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 | 2.25 | 2.32 | 100 | 0.548 | 0.652 | 14 |
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 | 6RX9 | 2.25 | 48.41 | 41073 | 2151 | 99.95 | 0.24215 | 0.24039 | 0.27596 | RANDOM | 52.613 |
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] | |
2.88 | -2.09 | -0.79 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.984 |
r_dihedral_angle_4_deg | 13.603 |
r_dihedral_angle_3_deg | 13.327 |
r_dihedral_angle_1_deg | 12.531 |
r_long_range_B_refined | 2.69 |
r_long_range_B_other | 2.69 |
r_angle_refined_deg | 1.148 |
r_angle_other_deg | 1.032 |
r_mcangle_it | 0.374 |
r_mcangle_other | 0.374 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5911 |
Nucleic Acid Atoms | |
Solvent Atoms | 128 |
Heterogen Atoms | 150 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |