7V1W
Difructose dianhydride I synthase/hydrolase (alphaFFase1) from Bifidobacterium dentium in complex with beta-D-arabinofuranose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4KQ7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293.15 | 20% PEG3350, 0.2 M di-sodium tartrate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 47.95 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 98.451 | α = 90 |
b = 156.707 | β = 110.66 |
c = 100.849 | 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 EIGER X 16M | 2019-09-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.000 | SLS | X06SA |
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 | 1.86 | 48.77 | 100 | 0.122 | 0.132 | 0.05 | 0.997 | 10.9 | 6.9 | 237104 | 15.05 |
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 | 1.87 | 1.9 | 100 | 0.842 | 0.912 | 0.489 | 0.811 | 2.4 | 6.8 |
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 | 4KQ7 | 1.86 | 48.77 | 224977 | 12087 | 99.95 | 0.1701 | 0.1683 | 0.2034 | RANDOM | 27.033 |
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] | |
0.02 | -0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.917 |
r_dihedral_angle_4_deg | 18.197 |
r_dihedral_angle_3_deg | 14.711 |
r_dihedral_angle_1_deg | 7.832 |
r_angle_refined_deg | 1.613 |
r_angle_other_deg | 1.364 |
r_chiral_restr | 0.081 |
r_bond_refined_d | 0.01 |
r_gen_planes_refined | 0.009 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 21768 |
Nucleic Acid Atoms | |
Solvent Atoms | 1748 |
Heterogen Atoms | 66 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
Aimless | data scaling |
MoRDa | phasing |