6R3U
Endo-levanase BT1760 mutant E221A from Bacteroides thetaiotaomicron complexed with levantetraose
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 282 | 16 mg/ml protein; 12-14% (w/v) PEG 6000, 0.5 mM ZnCl2, 0.1 M MES-NaOH, pH 6.5; 2:1 ratio |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.34 | 63.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.114 | α = 90 |
b = 112.334 | β = 90 |
c = 174.135 | γ = 90 |
Symmetry | |
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Space Group | I 2 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 PILATUS 6M | 2018-12-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALBA BEAMLINE XALOC | 0.98 | ALBA | XALOC |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 1.9 | 47.21 | 99.8 | 0.084 | 0.09 | 0.032 | 0.999 | 15.6 | 7.8 | 60697 | 30.02 |
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) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.9 | 1.97 | 99.2 | 1.129 | 1.208 | 0.424 | 0.74 | 1.9 | 7.9 |
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-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6R3R | 1.9 | 47.21 | 60564 | 1438 | 99.8 | 0.161 | 0.19 | 42.63 |
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 | 17.3702 |
f_angle_d | 1.0334 |
f_chiral_restr | 0.0661 |
f_bond_d | 0.0117 |
f_plane_restr | 0.0075 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3969 |
Nucleic Acid Atoms | |
Solvent Atoms | 326 |
Heterogen Atoms | 65 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
PHENIX | refinement |
XDS | data scaling |