6FX3
crystal structure of Pholiota squarrosa lectin in complex with a dodecasaccharide
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 292 | 3.4 M Na malonate pH5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48.59 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 101.744 | α = 90 |
b = 101.744 | β = 90 |
c = 101.744 | γ = 90 |
Symmetry | |
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Space Group | I 21 3 |
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 | 2017-12-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | 0.9793 | SOLEIL | PROXIMA 1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.7 | 41.54 | 100 | 0.05 | 0.018 | 1 | 32.8 | 17.3 | 19409 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.7 | 1.73 | 100 | 0.663 | 0.239 | 0.917 | 4.6 | 16.9 |
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 | PhoslOcta | 1.7 | 41 | 18434 | 973 | 99.95 | 0.15883 | 0.15733 | 0.18661 | RANDOM | 26.598 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 23.792 |
r_dihedral_angle_4_deg | 10.2 |
r_dihedral_angle_3_deg | 9.193 |
r_dihedral_angle_1_deg | 7.214 |
r_long_range_B_refined | 6.519 |
r_long_range_B_other | 6.103 |
r_scangle_other | 4.508 |
r_scbond_it | 2.968 |
r_scbond_other | 2.963 |
r_mcangle_other | 2.513 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 648 |
Nucleic Acid Atoms | |
Solvent Atoms | 137 |
Heterogen Atoms | 241 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |