8AGS
Cyclohexane epoxide soak of epoxide hydrolase from metagenomic source ch65 resulting in halogenated compound in the active site
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 291 | Morpheus crystallisation kit C1; 40% v/v PEG 500* MME; 20% w/v PEG 20000, thecrystal was soaked with cyclohexane epoxide substrate at pH 6.5 for 2 hours to produce halogenated product. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 41.06 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 69.21 | α = 90 |
b = 46.19 | β = 98 |
c = 92.14 | 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 | PIXEL | DECTRIS PILATUS 6M | 2018-08-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.97625 | Diamond | I03 |
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 | 1.61 | 46.19 | 97.5 | 0.999 | 12.2 | 3.2 | 73190 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.61 | 1.64 | 0.43 |
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 | 5ng7 | 1.61 | 45.663 | 73175 | 3603 | 97.448 | 0.182 | 0.1803 | 0.2226 | 33.552 |
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] | |
-1.032 | -1.534 | 0.244 | 1.173 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.828 |
r_dihedral_angle_4_deg | 23.874 |
r_dihedral_angle_3_deg | 16.664 |
r_lrange_it | 11.018 |
r_scangle_it | 10.36 |
r_scbond_it | 8.969 |
r_mcangle_it | 6.892 |
r_mcbond_it | 5.896 |
r_dihedral_angle_1_deg | 5.804 |
r_angle_refined_deg | 1.727 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4839 |
Nucleic Acid Atoms | |
Solvent Atoms | 300 |
Heterogen Atoms | 83 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |
Coot | model building |
BUSTER | refinement |
PARROT | phasing |