8BET
Structure of D188A-fructofuranosidase from Rhodotorula dairenesis in complex with sucrose
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 291 | 18% PEG 3350, 0.2 M MgCl2, 0.1 M BIS-TRIS pH 5.5 at 5.1 mg mL-1 concentration, 1:1 rate. Soaking: Mother liquor solution supplemented with 30 mM sucrose. 1h 15 min. Cryocooling: Mother liquor solution supplemented with 20% glycerol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.18 | 43.54 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 80.343 | α = 90 |
b = 112.813 | β = 104.74 |
c = 139.083 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 PILATUS 6M | KB Mirrors | 2021-06-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALBA BEAMLINE XALOC | 0.979264 | ALBA | XALOC |
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 | 2.38 | 45.69 | 99.8 | 0.114 | 0.124 | 0.047 | 0.996 | 11.8 | 6.7 | 96053 |
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 | 2.38 | 2.42 | 0.678 | 0.731 | 0.272 | 0.876 | 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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | 8BEQ | 2.38 | 45.69 | 91288 | 4728 | 99.78 | 0.1861 | 0.1843 | 0.2222 | RANDOM | 37.081 |
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] | |
-0.26 | -0.79 | 1.15 | -0.42 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.174 |
r_dihedral_angle_4_deg | 13.297 |
r_dihedral_angle_3_deg | 12.531 |
r_dihedral_angle_1_deg | 7.561 |
r_angle_refined_deg | 1.439 |
r_angle_other_deg | 1.388 |
r_chiral_restr | 0.06 |
r_bond_refined_d | 0.009 |
r_bond_other_d | 0.006 |
r_gen_planes_refined | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 16146 |
Nucleic Acid Atoms | |
Solvent Atoms | 694 |
Heterogen Atoms | 883 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
XDS | data scaling |
REFMAC | phasing |