6T9A
Crystal structrue of RSL W31FW76F lectin mutant in complex with L-fucose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2BT9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.2 | 293 | 23% PEG 6000, 0.1M Glycine, 0.1M Tris/HCl, pH 8.2 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.9 | 35.14 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 40.262 | α = 116.4 |
b = 42.105 | β = 94.54 |
c = 44.02 | γ = 115.49 |
Symmetry | |
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Space Group | P 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 PILATUS 2M | 2017-10-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.2 | 0.9184 | BESSY | 14.2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 37.15 | 96.4 | 0.053 | 0.053 | 0.071 | 0.048 | 0.994 | 8.3 | 2 | 14315 | 14315 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 2 | 2.11 | 95.3 | 0.16 | 0.047 | 0.063 | 0.041 | 0.933 | 2 |
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 | 2BT9 | 2 | 37.15 | 13517 | 789 | 96.31 | 0.1547 | 0.1522 | 0.1982 | RANDOM | 23.392 |
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] | |
-0.77 | -1.32 | -0.94 | 0.64 | 0.83 | 0.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.801 |
r_dihedral_angle_3_deg | 10.375 |
r_dihedral_angle_1_deg | 7.459 |
r_dihedral_angle_4_deg | 5.174 |
r_angle_refined_deg | 1.309 |
r_angle_other_deg | 1.137 |
r_chiral_restr | 0.038 |
r_gen_planes_refined | 0.004 |
r_bond_refined_d | 0.003 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1977 |
Nucleic Acid Atoms | |
Solvent Atoms | 255 |
Heterogen Atoms | 133 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
MOLREP | phasing |