8BEU
Structure of D188A-fructofuranosidase from Rhodotorula dairenensis in complex with raffinose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 8BEQ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 291 | 20% PEG 3350, 0.2 M NaCl, 0.1 M BIS-TRIS pH 5.5 at 5.5 mg ml-1 concentration, 2:1 rate. Soaking: Mother liquor solution supplemented with 30 mM raffinose. 2h Cryocooling: Mother liquor solution supplemented with 20% glycerol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 44.92 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.008 | α = 90 |
b = 114.544 | β = 104.58 |
c = 139.165 | 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 | 2021-06-19 | 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 | 2.27 | 46.29 | 99.9 | 0.132 | 0.144 | 0.055 | 0.993 | 9.1 | 6.8 | 113410 |
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 | 2.27 | 2.31 | 99.9 | 0.689 | 0.744 | 0.401 | 0.866 | 7 |
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 | 2.27 | 46.29 | 107654 | 5731 | 99.84 | 0.2082 | 0.2061 | 0.247 | RANDOM | 47.699 |
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] | |
-1.71 | -0.68 | 3.03 | -0.85 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.996 |
r_dihedral_angle_3_deg | 12.679 |
r_dihedral_angle_4_deg | 12.398 |
r_dihedral_angle_1_deg | 7.803 |
r_angle_other_deg | 1.483 |
r_angle_refined_deg | 1.445 |
r_chiral_restr | 0.06 |
r_gen_planes_refined | 0.007 |
r_bond_refined_d | 0.006 |
r_gen_planes_other | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 16133 |
Nucleic Acid Atoms | |
Solvent Atoms | 561 |
Heterogen Atoms | 920 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
XDS | data scaling |
REFMAC | phasing |