6S2B
Structure of beta-fructofuranosidase from Schwanniomyces occidentalis complexed with fructosyl-erythritol
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 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 transferred to a soaking solution containing mother liquor and 66 mM fructosyl-erythritol for 4 hours, and subsequently to a fresh drop supplemented with 25% ethylene glycol . |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.58 | 52.41 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.483 | α = 90 |
b = 92.54 | β = 104.71 |
c = 116.108 | 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 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 | 1.88 | 49.33 | 98.6 | 0.123 | 0.137 | 0.059 | 0.99 | 9.2 | 5.4 | 98961 | 17.6 |
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 | 1.88 | 1.91 | 97.9 | 0.63 | 0.7 | 0.3 | 0.773 | 3 | 5.4 |
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 | 1.88 | 49.33 | 94088 | 4859 | 98.42 | 0.15512 | 0.15391 | 0.17853 | RANDOM | 18.584 |
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] | |
1.21 | -0.36 | -0.09 | -0.82 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.722 |
r_dihedral_angle_3_deg | 12.585 |
r_dihedral_angle_4_deg | 11.969 |
r_dihedral_angle_1_deg | 8.177 |
r_long_range_B_refined | 4.836 |
r_long_range_B_other | 4.835 |
r_scangle_other | 3.3 |
r_mcangle_it | 2.061 |
r_mcangle_other | 2.06 |
r_scbond_it | 2.037 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8308 |
Nucleic Acid Atoms | |
Solvent Atoms | 849 |
Heterogen Atoms | 226 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |