2WYF
Crystal structure of PA-IL lectin complexed with aGal12bGal-O-Met at 2.4 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1OKO | PDB ENTRY 1OKO |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 4 | 15% PEG 6000, 1M LITHIUM CHLORIDE, 100MM CITRIC ACID PH 4.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.98 | 37.54 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 49.885 | ¦Á = 90 |
b = 99.788 | ¦Â = 100.77 |
c = 91.318 | ¦Ã = 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 CCD | 2008-03-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | ESRF | ID14-1 |
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 | 2.4 | 37.11 | 99.2 | 0.11 | 8.5 | 3.1 | 32401 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
1 | 2.4 | 2.53 | 99.8 | 0.35 | 3.1 | 3.1 |
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 | PDB ENTRY 1OKO | 2.4 | 89.8 | 32401 | 1718 | 99.06 | 0.1704 | 0.16574 | 0.25891 | RANDOM | 13.294 |
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] | |
-0.09 | -0.24 | 0.69 | -0.7 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.495 |
r_dihedral_angle_3_deg | 14.582 |
r_dihedral_angle_4_deg | 9.08 |
r_dihedral_angle_1_deg | 6.562 |
r_scangle_it | 2.524 |
r_scbond_it | 1.659 |
r_angle_refined_deg | 1.581 |
r_mcangle_it | 1.172 |
r_mcbond_it | 0.725 |
r_nbtor_refined | 0.31 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7185 |
Nucleic Acid Atoms | |
Solvent Atoms | 646 |
Heterogen Atoms | 176 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |