4WD2
Crystal structure of an aromatic amino acid aminotransferase from Burkholderia cenocepacia J2315
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3TAT | PDB entry 3tat |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 290 | Rigaku Reagents JCSG+ screen d1: 24% PEG 1500, 20% glycerol; BuceA.01471.a.B1.PS01824 at 20 mg/ml + 2.5mM pyridoxal phosphate; di rect cryo; tray 257500 d1, puck zba1-4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.81 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 59.22 | α = 90 |
b = 59.22 | β = 90 |
c = 200.27 | γ = 120 |
Symmetry | |
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Space Group | P 31 1 2 |
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 | RIGAKU SATURN 944+ | 2014-08-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.95 | 50 | 99.1 | 0.09 | 0.095 | 22.52 | 9.86 | 29633 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.95 | 2 | 90.9 | 0.346 | 0.387 | 4.72 | 4.8 |
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 (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 | FREE R-VALUE | PDB entry 3tat | 1.95 | 45.647 | 1.35 | 29568 | 1497 | 99.09 | 0.1183 | 0.1156 | 0.1514 | Random selection | 16.3048 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.602 |
f_angle_d | 0.893 |
f_chiral_restr | 0.035 |
f_bond_d | 0.005 |
f_plane_restr | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3009 |
Nucleic Acid Atoms | |
Solvent Atoms | 396 |
Heterogen Atoms | 24 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |