6QFD
The complex structure of hsRosR-S4 (vng0258/RosR-S4)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6FDH | The starting model for molecular replacement was VNG0258H/RosR (from KCl; PDB code 6FDH) and a DNA model derived from Mycobacterium tuberculosis MosR (PDB code 4FX4). |
experimental model | PDB | 4FX4 | The starting model for molecular replacement was VNG0258H/RosR (from KCl; PDB code 6FDH) and a DNA model derived from Mycobacterium tuberculosis MosR (PDB code 4FX4). |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | The complex crystallized from a buffer containing 20 mM HEPES, pH 7, 2 M KCl and 0.02% azide. Crystals grown with S4 (DNA/hsRosR ratio = 1.45) appeared after 3 days in wells containing 2.94 M (NH4)2SO4, 40 mM MnCl2 and 0.02% azide. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.74 | 60 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.805 | α = 81.53 |
b = 83.995 | β = 86.18 |
c = 88.876 | γ = 74.48 |
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 | PIXEL | DECTRIS PILATUS 2M | 2017-12-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 1.000030 | SLS | X06DA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rpim I (All) | 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 | 2.133 | 44.585 | 89.4 | 0.037 | 10 | 3.7 | 45836 |
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 | 2.133 | 2.356 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | The starting model for molecular replacement was VNG0258H/RosR (from KCl; PDB code 6FDH) and a DNA model derived from Mycobacterium tuberculosis MosR (PDB code 4FX4). | 2.133 | 44.585 | 1.96 | 45794 | 2308 | 63.76 | 0.211 | 0.2099 | 0.2318 | 77.923 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3667 |
Nucleic Acid Atoms | 2296 |
Solvent Atoms | 116 |
Heterogen Atoms | 143 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
STARANISO | data scaling |
PHASER | phasing |