4JXR
Crystal structure of a GNAT superfamily phosphinothricin acetyltransferase (Pat) from Sinorhizobium meliloti in complex with AcCoA
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 289 | 0.2 M di-Ammonium citrate pH 5.0, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.12 | 42.12 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.256 | α = 90 |
b = 80.978 | β = 90 |
c = 83.87 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 315r | mirrors | 2013-03-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.9792 | APS | 19-ID |
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 | 1.15 | 43.77 | 98.7 | 0.052 | 0.052 | 54.7 | 7.5 | 122819 | 122819 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.15 | 1.17 | 87 | 0.348 | 0.348 | 3.7 | 3.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | SAD | THROUGHOUT | 1.15 | 43.77 | 116559 | 116559 | 6152 | 98.69 | 0.11584 | 0.11472 | 0.1366 | RANDOM | 16.457 |
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] | |
0.68 | -0.18 | -0.51 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 40.197 |
r_dihedral_angle_2_deg | 31.12 |
r_sphericity_bonded | 14.953 |
r_dihedral_angle_4_deg | 13.018 |
r_dihedral_angle_3_deg | 11.834 |
r_rigid_bond_restr | 6.298 |
r_dihedral_angle_1_deg | 6.188 |
r_angle_other_deg | 2.762 |
r_angle_refined_deg | 1.922 |
r_chiral_restr | 0.105 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2833 |
Nucleic Acid Atoms | |
Solvent Atoms | 699 |
Heterogen Atoms | 99 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data collection |
HKL-3000 | phasing |
SHELXD | phasing |
SHELXE | model building |
MLPHARE | phasing |
DM | model building |
ARP/wARP | model building |
REFMAC | refinement |
Coot | model building |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
DM | phasing |