8AH3
DG04279 glycoside hydrolase family 172
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293.15 | 100 mM MOPS/HEPES pH 7.5, 20 mM 1,6-Hexanediol; 20 mM 1-Butanol 20 mM 1,2-Propanediol; 20 mM 2-Propanol; 20 mM 1,4-Butanediol; 20 mM 1,3-Propanedioalcohol, 20 % Etylene Glycol and 10 % PEG 8000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.55 | 51.81 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.15 | α = 90 |
b = 89.15 | β = 90 |
c = 289.32 | γ = 120 |
Symmetry | |
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Space Group | H 3 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 PILATUS 6M | 2020-08-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.9786 | Diamond | I24 |
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 | 1.4 | 68.112 | 99.9 | 0.078 | 0.086 | 0.036 | 0.999 | 12.7 | 10.2 | 87401 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.4 | 1.42 | 0.412 | 6.6 |
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 | 4KQ7 | 1.4 | 68.112 | 87400 | 4427 | 99.921 | 0.163 | 0.1622 | 0.1839 | 24.541 |
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] | |
0.865 | 0.432 | 0.865 | -2.805 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_6_deg | 17.712 |
r_dihedral_angle_3_deg | 13.062 |
r_dihedral_angle_2_deg | 12.547 |
r_dihedral_angle_1_deg | 7.685 |
r_lrange_it | 5.223 |
r_lrange_other | 5.174 |
r_scangle_it | 4.584 |
r_scangle_other | 4.584 |
r_scbond_it | 3.162 |
r_scbond_other | 3.161 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3043 |
Nucleic Acid Atoms | |
Solvent Atoms | 208 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
XDS | data scaling |
xia2 | data scaling |
pointless | data scaling |
Aimless | data scaling |
PHASER | phasing |
Coot | model building |
BUCCANEER | model building |
MolProbity | model building |
REFMAC | refinement |
XDS | data reduction |