8B73
Acetivibrio clariflavus beta-1,4-xylanase of Glycoside Hydrolase Family 10 (AcXyn10A).
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.4 | 293.15 | H6 conditions of JCSG+ HTS 0.1 M Ammonium acetate 0.1 M BIS-Tris, 17 % w/v PEG 10,000 109.79mM Xyltetraose (10X) with AcXynA protein in buffer containing 50mM NaCl, 20mM Tris-Cl |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.27243114 | 62.436615 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 80.566 | α = 90 |
b = 88.916 | β = 90 |
c = 173.479 | 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 | 100 | PIXEL | DECTRIS EIGER2 XE 16M | 2021-07-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9793 | Diamond | I03 |
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 | 2.24 | 89.58 | 99.81 | 0.166 | 0.173 | 0.05 | 0.997 | 8 | 12.7 | 61326 | 46.76 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.24 | 2.29 | 100 | 2.685 | 0.764 | 0.405 | 13.5 |
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 (All) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | SAD | FREE R-VALUE | 2.24 | 62.089 | 60339 | 3049 | 99.376 | 0.207 | 0.206 | 0.2316 | 52.222 |
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] | |
-0.412 | -0.407 | 0.819 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 13.934 |
r_dihedral_angle_6_deg | 13.832 |
r_dihedral_angle_1_deg | 6.278 |
r_dihedral_angle_2_deg | 5.448 |
r_lrange_it | 2.386 |
r_lrange_other | 2.38 |
r_scangle_it | 1.196 |
r_scangle_other | 1.195 |
r_mcangle_it | 1.174 |
r_mcangle_other | 1.174 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6578 |
Nucleic Acid Atoms | |
Solvent Atoms | 151 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
xia2.multiplex | data scaling |
PHASER | phasing |