6DJ8
Structure of DNA polymerase III subunit beta from Borrelia burgdorferi in complex with a natural product
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 290 | Morpheus Screen G4: 0.02M each Sodium formate, Ammonium acetate, Sodium citrate tribasic dihydrate, Sodium potassium tartrate tetrahydrate, Sodium oxamate: 0.1 M Imidazole/MES buffer pH 6.5, 12.5% MPD, 12.5% PEG 1000, 12.5% PEG3350: mixed 0.4:0.4 with BobuA.17987.a.B1.PW38224 at 20mg/ml. Co-crystallized with 1mM Griselmycin: direct cryo: tray 292391G4: puck YYX8-8 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.57 | 52.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 84.38 | α = 90 |
b = 68.29 | β = 113.7 |
c = 86.32 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | RAYONIX MX-300 | 2017-10-11 | 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) | Rrim 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 | 2.05 | 42 | 99.5 | 0.04 | 0.046 | 0.999 | 19.17 | 4.118 | 56445 | 47.42 |
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) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.05 | 42 | 96.7 | 0.487 | 0.033 | 0.998 | 2.36 | 3.674 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2.05 | 42 | 1.35 | 56397 | 1992 | 99.6 | 0.203 | 0.202 | 0.235 | 50.85 |
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 | 6158 |
Nucleic Acid Atoms | |
Solvent Atoms | 207 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHENIX | phasing |