8TRX
Crystal structure of a CE15 glucuronoyl esterase from Piromyces rhizinflatus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4G4G |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7.5 | 298 | 20% PEG10000, 100 mM HEPES, pH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.19 | 70.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 139.68 | α = 90 |
b = 139.68 | β = 90 |
c = 125.83 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 | 80 | PIXEL | DECTRIS PILATUS 6M | 2019-02-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | 1.00334 | CLSI | 08ID-1 |
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 | 2.54 | 46.745 | 99.96 | 0.08133 | 0.08558 | 0.999 | 19.03 | 10.4 | 45952 | 59.7 |
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 | 2.54 | 2.71 | 100 | 0.82 | 0.862 | 0.858 | 2.76 | 10.568 |
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 | FREE R-VALUE | 2.54 | 46.745 | 1.35 | 45939 | 2296 | 99.97 | 0.2311 | 0.229 | 0.2689 | 62.8856 |
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 | 3.106 |
f_angle_d | 1.083 |
f_chiral_restr | 0.061 |
f_bond_d | 0.01 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5829 |
Nucleic Acid Atoms | |
Solvent Atoms | 83 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data scaling |
XDS | data reduction |
PHASER | phasing |