6NWZ
Crystal structure of Agd3 a novel carbohydrate deacetylase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 1.7 % (w/v) PEG 400, 15 % (v/v) glycerol, 1.7 M ammonium sulfate, 0.25 % (w/v) PEG3350, 85 mM HEPES pH 7.5 |
2 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 1.7 % (w/v) PEG 400, 15 % (v/v) glycerol, 1.7 M ammonium sulfate, 0.25 % (w/v) PEG3350, 85 mM HEPES pH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.88 | 68.29 |
3.88 | 68.29 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 77.97 | α = 90 |
b = 77.97 | β = 90 |
c = 640.31 | γ = 120 |
Symmetry | |
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Space Group | P 61 2 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 | PIXEL | DECTRIS EIGER X 16M | 2017-07-11 | M | SINGLE WAVELENGTH | ||||||
2 | 2 | x-ray | 100 | PIXEL | DECTRIS EIGER X 16M | 2017-07-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 17-ID-1 | 1.28308 | NSLS-II | 17-ID-1 |
2 | SYNCHROTRON | NSLS-II BEAMLINE 17-ID-1 | 1.28308 | NSLS-II | 17-ID-1 |
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 | 2.59 | 29.87 | 86.13 | 0.02467 | 0.03489 | 0.02467 | 0.999 | 17.91 | 2 | 37314 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.59 | 2.694 | 13.57 | 0.364 | 0.364 | 0.257 | 0.968 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | SAD | THROUGHOUT | 2.6 | 29.865 | 1.36 | 32191 | 1690 | 86.17 | 0.1923 | 0.1895 | 0.2423 | Random | 47.4631 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5095 |
Nucleic Acid Atoms | |
Solvent Atoms | 120 |
Heterogen Atoms | 90 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
SHELX | phasing |
PHASER | phasing |
PDB_EXTRACT | data extraction |