3APB
Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with iodide
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293.15 | 0.55mM protein, 10mM Hepes-NaOH, 50mM sodium chloride, 0.5mM DTT, 125mM ammonium fluoride, 8% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.78 | 55.77 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 65.591 | α = 90 |
b = 75.869 | β = 90 |
c = 77.901 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | RIGAKU JUPITER 210 | 2005-06-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL38B1 | 1.30000 | SPring-8 | BL38B1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 1.947 | 38.954 | 99.9 | 28969 | 28969 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1.94 | 2.01 | 99.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | SAD | THROUGHOUT | 1.95 | 38.95 | 27561 | 27561 | 1408 | 99.51 | 0.20342 | 0.20151 | 0.24198 | RANDOM | 23.384 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.2 | -0.8 | 0.6 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.673 |
r_dihedral_angle_4_deg | 18.47 |
r_dihedral_angle_3_deg | 12.442 |
r_dihedral_angle_1_deg | 6.498 |
r_scangle_it | 3.277 |
r_scbond_it | 1.962 |
r_angle_refined_deg | 1.318 |
r_mcangle_it | 1.293 |
r_angle_other_deg | 0.81 |
r_mcbond_it | 0.689 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2424 |
Nucleic Acid Atoms | |
Solvent Atoms | 162 |
Heterogen Atoms | 29 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
SHARP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |