1LU2
DOLICHOS BIFLORUS SEED LECTIN IN COMPLEX WITH THE BLOOD GROUP A TRISACCHARIDE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1FAT | PDB ENTRY 1FAT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6.6 | 100 MM NACACO PH 6.6 15% (W/V) PEG-ME 5000 10 MM BLOOD GROUP A TRISACCHARIDE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 55 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 96.73 | α = 90 |
b = 108 | β = 124.67 |
c = 80.96 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 293 | IMAGE PLATE | MARRESEARCH | 1998-01-16 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.8 | 15 | 85.2 | 0.11 | 10.7 | 2.7 | 14331 | 29.7 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.8 | 2.91 | 85.8 | 0.274 | 3.1 | 1.8 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | PDB ENTRY 1FAT | 2.8 | 15 | 14331 | 1457 | 85.3 | 0.191 | 0.191 | 0.219 | RANDOM | 32.1 |
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] | |
1.03 | -0.76 | -0.16 | -0.87 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 29.1 |
x_scangle_it | 3.67 |
x_mcangle_it | 2.48 |
x_scbond_it | 2.3 |
x_angle_deg | 1.6 |
x_mcbond_it | 1.41 |
x_improper_angle_d | 0.74 |
x_bond_d | 0.008 |
x_bond_d_na | |
x_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3784 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
X-PLOR | model building |
X-PLOR | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
X-PLOR | phasing |