4YM0
Crystal structure of the human galectin-4 C-terminal carbohydrate recognition domain in complex with lacto-N-tetraose (LNT)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293.15 | 1.2 M ammonium sulfate, 0.1 M HEPES pH 7.0, 4 % v/v PEG 400 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.96 | 37.18 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 45.189 | α = 90 |
b = 130.67 | β = 96.35 |
c = 45.271 | 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 | CCD | ADSC QUANTUM 210r | 2013-10-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX1 | 0.9537 | Australian Synchrotron | MX1 |
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 | 2.3 | 44.99 | 98.6 | 0.028 | 0.016 | 0.999 | 35.2 | 4.1 | 22849 |
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 | 2.3 | 2.38 | 88.8 | 0.106 | 0.071 | 0.978 | 10 | 3.1 | 2032 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2.3 | 42.54 | 21708 | 1113 | 98.09 | 0.1738 | 0.1721 | 0.2079 | RANDOM | 28.378 |
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] | |
3.89 | -4.07 | -1.61 | -2.28 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.481 |
r_dihedral_angle_3_deg | 14.915 |
r_dihedral_angle_4_deg | 14.262 |
r_dihedral_angle_1_deg | 6.687 |
r_angle_other_deg | 2.05 |
r_mcangle_it | 1.82 |
r_angle_refined_deg | 1.366 |
r_mcbond_it | 0.965 |
r_mcbond_other | 0.965 |
r_chiral_restr | 0.107 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4353 |
Nucleic Acid Atoms | |
Solvent Atoms | 128 |
Heterogen Atoms | 151 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHASER | phasing |