3LM1
Crystal Structure Analysis of Maclura pomifera agglutinin complex with p-nitrophenyl-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 | 0.5M of lithium sulfate, 12% PEG 8000, 1% octyl-beta-D-glucopyranoside, 0.1M Hepes, pH 7.0 in the reservoir solution. The sitting drop is made by protein (28mg/mL) and equal volumn of reservoir solution in the presence of p-nitrophenyl-alpha-GalNAc., VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.53 | 65.18 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 69.09 | α = 90 |
b = 133.29 | β = 90 |
c = 200.05 | 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 | 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 | 1.9 | 29.8 | 83.8 | 0.039 | 24.7 | 3 | 145978 | 122330 | 2 | 2 | 36.7 |
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) | |||||||||||
1.9 | 1.97 | 46.6 | 0.29 | 4.5 | 2.1 | 6716 |
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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1JOT | 2.1 | 20 | 2 | 108366 | 99067 | 9650 | 91.4 | 0.244 | 0.223 | 0.223 | 0.244 | random | 26.595 |
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] | |
2.508 | -0.445 | -2.064 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_scangle_it | 2.622 |
c_scbond_it | 1.804 |
c_mcangle_it | 1.76 |
c_mcbond_it | 1.143 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9263 |
Nucleic Acid Atoms | |
Solvent Atoms | 879 |
Heterogen Atoms | 168 |
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 |