8K2I
Crystal structure of Group 2 Oligosaccharide/Monosaccharide-releasing beta-N-acetylhexosaminidase NgaAt from Arabidopsis thaliana in complex with GlcNAc-thiazoline
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293.15 | 0.2 M Magnesium chloride hexahydrate, 0.1 M Hepes-Na pH 7.5, 25% w/v Polyethylene glycol 3,350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 48.85 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 69.284 | ¦Á = 90 |
b = 133.833 | ¦Â = 90 |
c = 150.723 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 9M | 2022-10-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL32XU | 1.0000 | SPring-8 | BL32XU |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.5 | 48.13 | 100 | 0.994 | 7.4 | 13.9 | 49358 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.5 | 2.58 | 0.684 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2.5 | 47.71 | 46789 | 2489 | 99.95 | 0.16084 | 0.15719 | 0.22989 | RANDOM | 53.75 |
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] | |
2.46 | -3.95 | 1.49 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 16.936 |
r_dihedral_angle_2_deg | 16.362 |
r_long_range_B_other | 11.749 |
r_long_range_B_refined | 11.737 |
r_scangle_other | 10.175 |
r_mcangle_it | 8.865 |
r_mcangle_other | 8.865 |
r_dihedral_angle_1_deg | 8.351 |
r_scbond_it | 7.829 |
r_scbond_other | 7.828 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8911 |
Nucleic Acid Atoms | |
Solvent Atoms | 241 |
Heterogen Atoms | 43 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |