3LLZ
Crystal Structure Analysis of Maclura pomifera agglutinin complex with Gal-beta-1,3-GalNAc
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1JOT | PDB ENTRY 1JOT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 298 | 0.5 M of lithium sulfate, 12% PEG 8000, 1% octyl-beta-D-glucopyranoside, 0.1M Hepes, pH 7.0 in the resevoir solution. the sitting drop is made by protein (28mg/mL) and equal volumn of reservoir solution in the presence of Gal-beta-1,3-GalNAc., VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.91 | 57.78 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 66.54 | α = 90 |
b = 66.54 | β = 90 |
c = 147.95 | γ = 120 |
Symmetry | |
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Space Group | P 64 2 2 |
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 4r | mirrors | 2000-06-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4A | 0.9793 | NSLS | X4A |
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 | 1.5 | 26.3 | 98.2 | 0.052 | 35 | 8.1 | 31933 | 31358 | 2 | 2 | 23.36 |
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) | |||||||||||
1.5 | 1.55 | 86.6 | 0.199 | 6.8 | 4.7 | 2693 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1JOT | 1.55 | 20 | 2 | 28958 | 27054 | 2175 | 93.4 | 0.222 | 0.21 | 0.227 | random | 19.407 |
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] | |
-3.343 | -1.908 | -3.343 | 6.686 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_scangle_it | 2.963 |
c_scbond_it | 2.02 |
c_mcangle_it | 1.608 |
c_mcbond_it | 1.097 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1151 |
Nucleic Acid Atoms | |
Solvent Atoms | 155 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
PDB_EXTRACT | data extraction |
APEX | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
AMoRE | phasing |