3ABR
Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-Cbl (substrate-free form)
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), 0.1 M imidazole-HCl, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.01 | 69.36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 244.12 | α = 90 |
b = 244.12 | β = 90 |
c = 77.15 | 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 | CCD | ADSC QUANTUM 210 | mirrors | 2008-06-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 1.0000 | SPring-8 | BL41XU |
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 | 2.1 | 50 | 94.6 | 0.078 | 12.7 | 3.3 | 144730 | 144730 |
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 | 2.1 | 2.15 | 91.1 | 0.299 | 3.5 | 2.6 | 9260 |
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 | 2.1 | 42.29 | 137417 | 7300 | 94.52 | 0.24962 | 0.24773 | 0.28519 | RANDOM | 11.382 |
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] | |
0.81 | 0.4 | 0.81 | -1.21 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.668 |
r_dihedral_angle_4_deg | 19.513 |
r_dihedral_angle_3_deg | 16.687 |
r_dihedral_angle_1_deg | 7.094 |
r_angle_refined_deg | 1.169 |
r_chiral_restr | 0.226 |
r_scangle_it | 0.195 |
r_mcangle_it | 0.191 |
r_scbond_it | 0.126 |
r_mcbond_it | 0.111 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10760 |
Nucleic Acid Atoms | |
Solvent Atoms | 1000 |
Heterogen Atoms | 225 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |