6M5Z
Catalytic domain of GH30 xylanase C from Talaromyces cellulolyticus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 293 | 14% PEG 8000, 100 mM MES, 200 mM calcium acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.03 | 39.35 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 38.559 | α = 79.74 |
b = 52.305 | β = 88.6 |
c = 98.535 | γ = 84.3 |
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 EIGER X 16M | 2018-12-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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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 | 1.65 | 50 | 96.8 | 0.073 | 0.087 | 0.046 | 0.998 | 11.8 | 3.5 | 87809 | -3 | 16.48 |
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 | 1.65 | 1.71 | 93.5 | 0.633 | 0.748 | 0.395 | 0.703 | 2 | 3.5 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 6IUJ | 1.65 | 49.01 | 83430 | 4392 | 96.4 | 0.1485 | 0.1811 | RANDOM | 15.238 |
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] | |
0.15 | 0.11 | -0.58 | 0.24 | 0.55 | -0.17 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.364 |
r_dihedral_angle_1_deg | 13.222 |
r_dihedral_angle_4_deg | 11.731 |
r_dihedral_angle_3_deg | 11.048 |
r_long_range_B_refined | 3.748 |
r_long_range_B_other | 3.657 |
r_scangle_other | 2.881 |
r_scbond_it | 1.964 |
r_scbond_other | 1.964 |
r_mcangle_other | 1.819 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6462 |
Nucleic Acid Atoms | |
Solvent Atoms | 642 |
Heterogen Atoms | 50 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data processing |
XDS | data scaling |
MOLREP | phasing |
XDS | data reduction |