5BOV
Crystal structure of a putative epoxide hydrolase (KPN_01808) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.60 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.1M bicine pH 9, 30% polyethylene glycol 6000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 43.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.199 | α = 101 |
b = 81.866 | β = 106.9 |
c = 89.925 | γ = 100.84 |
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 | CCD | MARMOSAIC 325 mm CCD | Vertical focusing mirror; double crystal Si(111) monochromator | 2015-03-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL14-1 | 0.97907 | SSRL | BL14-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 1.6 | 42.848 | 96.8 | 0.078 | 0.091 | 11.66 | 3.916 | 146333 | -3 | 15.778 |
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) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.6 | 1.66 | 95.2 | 0.655 | 0.758 | 2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.6 | 42.848 | 146328 | 7372 | 96.94 | 0.1498 | 0.1485 | 0.1739 | RANDOM | 17.638 |
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] | |
0.17 | -0.49 | -0.51 | 0.22 | 0.04 | 0.09 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.868 |
r_dihedral_angle_4_deg | 16.128 |
r_dihedral_angle_3_deg | 10.562 |
r_dihedral_angle_1_deg | 6.056 |
r_angle_other_deg | 1.91 |
r_angle_refined_deg | 1.785 |
r_mcangle_it | 1.397 |
r_mcbond_it | 0.882 |
r_mcbond_other | 0.881 |
r_chiral_restr | 0.109 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9395 |
Nucleic Acid Atoms | |
Solvent Atoms | 1880 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
PDB_EXTRACT | data extraction |
SHELX | phasing |
SHARP | phasing |
XDS | data reduction |
XSCALE | data scaling |
REFMAC | refinement |
SHELXD | phasing |