5TRX
Room temperature structure of an extradiol ring-cleaving dioxygenase from B.fuscum determined using serial femtosecond crystallography
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 5.8 | 293 | Precipitant added to enzyme solution at 1:1 ratio: 12-14% PEG6000, 0.1-0.14 M calcium chloride, and 0.1 M MES pH 5.8. Crystallization carried out in a tube to produce saturated slurry of micro crystals |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.63 | 53.28 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 111.57 | α = 90 |
b = 154.86 | β = 90 |
c = 101.8 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 293 | PIXEL | CS-PAD CXI-2 | 2015-06-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE CXI | 1.5498 | SLAC LCLS | CXI |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.38 | 34.5 | 99.9 | 0.81 | 2.43 | 26.5 | 71326 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.38 | 2.47 | 99.5 | 0.45 | 3.42 | 13 |
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 | FOURIER SYNTHESIS | THROUGHOUT | 3OJT | 2.38 | 20 | 67578 | 3568 | 99.69 | 0.1869 | 0.1845 | 0.2321 | RANDOM | 43.583 |
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] | |
0.13 | 0.66 | -0.79 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_mcangle_it | 2.259 |
r_mcbond_it | 1.511 |
r_mcbond_other | 1.511 |
r_angle_refined_deg | 1.358 |
r_angle_other_deg | 0.816 |
r_chiral_restr | 0.078 |
r_bond_refined_d | 0.011 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | 0.001 |
r_gen_planes_other | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11596 |
Nucleic Acid Atoms | |
Solvent Atoms | 439 |
Heterogen Atoms | 9 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CrystFEL | data scaling |
CrystFEL | data reduction |