3ABS
Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with adeninylpentylcobalamin and ethanolamine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3ABO | PDB ID 3ABO |
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 |
3.94 | 68.81 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 242.73 | ¦Á = 90 |
b = 242.73 | ¦Â = 90 |
c = 76.66 | ¦Ã = 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 | CCD | ADSC QUANTUM 270 | mirrors | 2008-12-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-17A | 1.0000 | Photon Factory | BL-17A |
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 | 50 | 98.3 | 0.101 | 21.9 | 9.6 | 120002 | 120002 |
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 | 2.3 | 85 | 0.516 | 2.47 | 4.4 | 6841 |
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 ID 3ABO | 2.25 | 50 | 113966 | 6020 | 98.23 | 0.21533 | 0.21378 | 0.24439 | RANDOM | 20.25 |
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] | |
-0.51 | -0.25 | -0.51 | 0.76 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.247 |
r_dihedral_angle_4_deg | 16.47 |
r_dihedral_angle_3_deg | 14.899 |
r_scangle_it | 8.279 |
r_scbond_it | 5.984 |
r_dihedral_angle_1_deg | 5.111 |
r_mcangle_it | 2.402 |
r_mcbond_it | 1.543 |
r_angle_refined_deg | 1.187 |
r_chiral_restr | 0.066 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10760 |
Nucleic Acid Atoms | |
Solvent Atoms | 660 |
Heterogen Atoms | 261 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |