3VXC
Crystal Structure of Xylobiose-BxlE complex from Streptomyces thermoviolaceus OPC-520
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 3.2 | 293 | 25% PEG 3350, 0.1M citrate, 15% glycerol, pH 3.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.94 | 36.71 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 103.672 | α = 90 |
b = 163.157 | β = 90 |
c = 42.931 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | IMAGE PLATE | RIGAKU RAXIS VII | M | MAD | |||||||
2 | 1 | x-ray | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | SPring-8 | BL41XU | |
2 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.78 | 45 | 98.1 | 0.071 | 70761 | 69417 | 2 | 1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 1.85 | 33.81 | 59174 | 3111 | 98.46 | 0.17026 | 0.16802 | 0.21282 | RANDOM | 15.681 |
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 |
r_dihedral_angle_2_deg | 36.694 |
r_dihedral_angle_4_deg | 16.699 |
r_dihedral_angle_3_deg | 14.35 |
r_dihedral_angle_1_deg | 6.117 |
r_scangle_it | 5.394 |
r_scbond_it | 3.548 |
r_mcangle_it | 2.009 |
r_angle_refined_deg | 1.816 |
r_mcbond_it | 1.171 |
r_chiral_restr | 0.134 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6074 |
Nucleic Acid Atoms | |
Solvent Atoms | 466 |
Heterogen Atoms | 38 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |