6S1T
Structure of beta-fructofuranosidase from Schwanniomyces occidentalis complexed with sucrose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3KF3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 291 | 20% PEG 6000, 0.2 M MgCl2, and 0.1 M HEPES pH 7.0, by mixing 1 uL of protein with 0.5 uL of mother liquor. Crystals were soaked in mother liquor supplemented with 83 mM fructosyl-manitol, contaminated with sucrose. Cryoprotectant mother liquor supplemented with 25% ethylene glycol. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.63 | 53.24 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.903 | α = 90 |
b = 93.201 | β = 104.9 |
c = 116.615 | 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 PILATUS3 S 6M | KB focusing mirrors | 2016-06-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALBA BEAMLINE XALOC | 0.979260 | 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 | 2.09 | 49.74 | 99.9 | 0.138 | 0.156 | 0.07 | 0.981 | 8.6 | 5 | 74544 | 17.4 |
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 | 2.09 | 2.13 | 99.8 | 0.569 | 0.64 | 0.286 | 0.802 | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 3KF3 | 2.09 | 49.74 | 70862 | 3606 | 99.79 | 0.1768 | 0.17495 | 0.21362 | RANDOM | 19.547 |
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] | |
1.95 | -0.55 | -0.66 | -0.87 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.161 |
r_dihedral_angle_4_deg | 15.199 |
r_dihedral_angle_3_deg | 13.658 |
r_dihedral_angle_1_deg | 7.472 |
r_long_range_B_refined | 4.749 |
r_long_range_B_other | 4.678 |
r_scangle_other | 3.29 |
r_mcangle_it | 2.214 |
r_mcangle_other | 2.214 |
r_scbond_it | 1.993 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8308 |
Nucleic Acid Atoms | |
Solvent Atoms | 794 |
Heterogen Atoms | 248 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |