7PUG
GH115 alpha-1,2-glucuronidase in complex with xylopentaose
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 0.2 M CaCl2, 0.1 M HEPES pH 7.5 and 28% PEG400 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.47 | 72.47 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 148.63 | α = 90 |
b = 148.63 | β = 90 |
c = 272.79 | γ = 120 |
Symmetry | |
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Space Group | P 61 2 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 | 100 | PIXEL | DECTRIS EIGER2 X 16M | 2019-05-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) | 1.0332 | PETRA III, EMBL c/o DESY | P14 (MX2) |
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 | 2.66 | 65.26 | 99.94 | 1 | 17.87 | 16.8 | 51774 |
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 | 2.66 | 2.78 | 0.37 |
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 | 4C90 | 2.66 | 65.26 | 1.34 | 51754 | 2574 | 99.95 | 0.1758 | 0.174 | 0.2104 | 99.06 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 21.544 |
f_angle_d | 0.9321 |
f_chiral_restr | 0.0555 |
f_plane_restr | 0.0082 |
f_bond_d | 0.0079 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6762 |
Nucleic Acid Atoms | |
Solvent Atoms | 298 |
Heterogen Atoms | 62 |
Software
Software | |
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Software Name | Purpose |
MxCuBE | data collection |
xia2 | data scaling |
Coot | model building |
PHENIX | phasing |
PHENIX | refinement |
xia2 | data reduction |