4EFF
Crystal structure of aromatic-amino-acid aminotransferase from Burkholderia pseudomallei
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3FSL | PDB ENTRY 3FSL, CHAIN A |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | Emerald Bio JCSG+ screen: 14.4% PEG8000, 160 mM calcium acetate, 20% glycerol, Bupse.01471.a.A1 PW 34948 at 36.1 mg/mL, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.19 | 43.95 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 66.19 | α = 90 |
b = 66.19 | β = 90 |
c = 156.86 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
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 | MARMOSAIC 300 mm CCD | 2012-03-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97860 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.85 | 50 | 99.5 | 0.078 | 0.078 | 20.49 | 7.3 | 34894 | 34726 | -3 | 22.96 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.85 | 1.9 | 100 | 0.524 | 0.524 | 3.9 | 7.2 | 2525 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 3FSL, CHAIN A | 1.85 | 50 | 34894 | 34713 | 1746 | 0.187 | 0.187 | 0.185 | 0.216 | RANDOM | 14.51 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.13 | 0.06 | 0.13 | -0.19 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.034 |
r_dihedral_angle_4_deg | 15.42 |
r_dihedral_angle_3_deg | 12.701 |
r_dihedral_angle_1_deg | 5.423 |
r_angle_refined_deg | 1.526 |
r_angle_other_deg | 0.962 |
r_chiral_restr | 0.087 |
r_bond_refined_d | 0.013 |
r_gen_planes_refined | 0.007 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2789 |
Nucleic Acid Atoms | |
Solvent Atoms | 285 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |