7VU9
Pholiota squarrosa lectin (PhoSL) in complex with fucose(alpha1-6)[GlcNAc(beta1-4)]GlcNAc
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6A86 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | 4.3 M sodium formate (pH 7.0) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.98 | 58.69 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 126.739 | α = 90 |
b = 127.057 | β = 90 |
c = 39.418 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 2 |
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 | 95 | PIXEL | DECTRIS EIGER X 16M | 2019-10-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-17A | 1.0 | Photon Factory | BL-17A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.154 | 44.87 | 99.5 | 0.087 | 0.996 | 9.18 | 3.5 | 17730 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.154 | 2.28 | 99.3 | 0.661 | 0.684 | 1.81 | 3.43 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6A86 | 2.154 | 44.865 | 17729 | 887 | 99.842 | 0.182 | 0.1788 | 0.2446 | 38.896 |
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] | |
0.064 | -0.041 | -0.023 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 26.7 |
r_dihedral_angle_other_3_deg | 26.075 |
r_dihedral_angle_1_deg | 18.712 |
r_dihedral_angle_3_deg | 16.832 |
r_lrange_other | 7.943 |
r_lrange_it | 7.923 |
r_scangle_it | 6.243 |
r_scangle_other | 6.242 |
r_mcangle_it | 5.139 |
r_mcangle_other | 5.138 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1878 |
Nucleic Acid Atoms | |
Solvent Atoms | 154 |
Heterogen Atoms | 252 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |