6GRW
Glucuronoyl Esterase from Opitutus terrae (Au derivative)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 293.15 | Reservoir composition for crystal growth: 0.03M Magnesium chloride, 0.03 M calcium chloride, 0.05M imidazole, 0.05M MES, 10% v/v MPD, 10% w/v PEG 1000, 10% v/w PEG 3500P. Heavy atom derivatization: 1.2uL crystallization mother liquor containing 0.5mM KAu(CN)2 added to drop containing crystals. Drop size and composition: Sitting drops of 0.4ul were mixed in a protein:reservoir volume ratio of 1:1 using 45 mg/mL of OtCE15A in 20 mM TRIS pH 8.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.96 | 37.16 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 43.693 | α = 76.573 |
b = 44.608 | β = 67.172 |
c = 50.558 | γ = 70.648 |
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 6M | 2017-08-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, DESY BEAMLINE P11 | 0.979 | PETRA III, DESY | P11 |
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 | 1.5 | 46.27 | 95.9 | 0.042 | 0.05 | 0.999 | 16.69 | 3.55 | 50802 | 14.57 |
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 | 1.5 | 1.59 | 93.3 | 0.314 | 0.37 | 0.923 | 3.4 | 3.6 |
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 | FREE R-VALUE | Structure under deposition | 1.5 | 46.27 | 1.99 | 50799 | 2101 | 96.1 | 0.1355 | 0.1345 | 0.1585 | 20.16 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 17.5942 |
f_angle_d | 1.0928 |
f_chiral_restr | 0.0764 |
f_plane_restr | 0.0092 |
f_bond_d | 0.0083 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3073 |
Nucleic Acid Atoms | |
Solvent Atoms | 402 |
Heterogen Atoms | 33 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
Coot | model building |
XDS | data reduction |
PHENIX | phasing |
XSCALE | data scaling |