6R5V
The crystal structure of Glycoside Hydrolase BglX inactive mutant D286N from P. aeruginosa in complex with xylotriose
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 291 | 100 mM Bis Tris, pH 5.5, 17% PEG 10000 and 100 mM ammonium acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.24 | 45.11 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 70.955 | α = 65.55 |
b = 73.668 | β = 73.46 |
c = 81.444 | γ = 69.66 |
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 | 2017-09-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALBA BEAMLINE XALOC | 0.979257 | ALBA | XALOC |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rpim 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 | 1.8 | 45.27 | 96.3 | 0.08 | 8.1 | 3 | 123955 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.8 | 1.83 | 0.42 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 5TF0 | 1.8 | 45.27 | 117725 | 6198 | 96.3 | 0.16451 | 0.16281 | 0.19654 | RANDOM | 19.184 |
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] | |
0.33 | 0.19 | -0.83 | -0.17 | 0.83 | 0.23 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.874 |
r_dihedral_angle_4_deg | 18.267 |
r_dihedral_angle_3_deg | 13.578 |
r_dihedral_angle_1_deg | 6.847 |
r_long_range_B_refined | 6.137 |
r_long_range_B_other | 6.137 |
r_scangle_other | 4.127 |
r_scbond_it | 2.623 |
r_scbond_other | 2.623 |
r_mcangle_it | 2.244 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11248 |
Nucleic Acid Atoms | |
Solvent Atoms | 1025 |
Heterogen Atoms | 64 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |