6KRN
Crystal structure of GH30 xylanase B from Talaromyces cellulolyticus expressed by Pichia pastoris in complex with aldotriuronic acid
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.3 | 293 | PEG 3350, HEPES, magnesium chloride |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.49 | 50.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.251 | α = 90 |
b = 78.7 | β = 90 |
c = 118.418 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 173 | PIXEL | DECTRIS EIGER X 16M | 2019-06-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | 0.9 | SPring-8 | BL44XU |
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 | 1.653 | 33.41 | 99.41 | 0.04648 | 0.05262 | 0.02424 | 0.999 | 15.35 | 4.5 | 71087 | 22.31 |
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 | 1.653 | 1.712 | 99.03 | 0.458 | 0.5184 | 0.2389 | 0.847 | 2.34 | 4.5 |
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-Factor (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6IUJ | 1.653 | 33.41 | 71087 | 3554 | 99.496 | 0.171 | 0.1695 | 0.1897 | 23.318 |
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] | |
1.213 | 0.101 | -1.314 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.378 |
r_dihedral_angle_4_deg | 16.856 |
r_dihedral_angle_3_deg | 12.785 |
r_dihedral_angle_1_deg | 6.222 |
r_lrange_it | 4.876 |
r_lrange_other | 4.77 |
r_scangle_it | 4.262 |
r_scangle_other | 4.261 |
r_scbond_it | 3.257 |
r_scbond_other | 3.257 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3517 |
Nucleic Acid Atoms | |
Solvent Atoms | 498 |
Heterogen Atoms | 249 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
MOLREP | phasing |