3AO0
Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-CBL and (S)-2-amino-1-propanol
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3ABR | PDB ENTRY 3ABR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.3 | 277 | 6.0-7.0% (W/V) PEG 4000, 24-26 % (V/V) GLYCEROL, 1.0 % (V/V) 2-METHYL-2,4-PENTANEDIOL (MPD),0.1M IMIDAZOLE-HCL, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.21 | 70.81 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 243.85 | α = 90 |
b = 243.85 | β = 90 |
c = 76.806 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
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 | IMAGE PLATE | BRUCKER DIP-6040 | MIRRORS | 2008-07-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | SPring-8 | BL44XU |
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 | 2.25 | 48 | 98.5 | 0.099 | 11.3 | 4.2 | 121794 | 121794 |
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 | 2.25 | 2.31 | 93.3 | 0.481 | 1.95 | 2.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | MR | THROUGHOUT | PDB ENTRY 3ABR | 2.25 | 48 | 115669 | 115669 | 6112 | 98.45 | 0.236 | 0.236 | 0.235 | 0.257 | RANDOM | 46.737 |
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] | |
-0.11 | -0.06 | -0.11 | 0.17 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.215 |
r_dihedral_angle_3_deg | 19.936 |
r_dihedral_angle_4_deg | 19.699 |
r_dihedral_angle_1_deg | 9.666 |
r_scangle_it | 3.511 |
r_scbond_it | 2.349 |
r_mcangle_it | 1.198 |
r_angle_refined_deg | 0.83 |
r_mcbond_it | 0.699 |
r_chiral_restr | 0.22 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10760 |
Nucleic Acid Atoms | |
Solvent Atoms | 592 |
Heterogen Atoms | 193 |
Software
Software | |
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Software Name | Purpose |
BSS | data collection |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |