5IWQ
Crystal structure of aspartate aminotransferase (AspAT) from Corynebacterium glutamicum ATCC 13032
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3D6K |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | PEG 3350, Ammonium citrate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.46 | 50.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 103.388 | α = 90 |
b = 53.521 | β = 104.23 |
c = 170.224 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | ADSC | 2014-12-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PAL/PLS BEAMLINE 7A (6B, 6C1) | 0.97934 | PAL/PLS | 7A (6B, 6C1) |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.999 | 165 | 97.7 | 41.61 | 3.6 | 56893 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2 | 2.03 |
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 | 3D6K | 2 | 165 | 56893 | 3050 | 97.44 | 0.1509 | 0.1484 | 0.1986 | RANDOM | 14.498 |
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] | |
-0.19 | -0.89 | 1.28 | -0.57 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.289 |
r_dihedral_angle_4_deg | 13.717 |
r_dihedral_angle_3_deg | 12.364 |
r_dihedral_angle_1_deg | 6.458 |
r_angle_refined_deg | 1.888 |
r_mcangle_it | 1.824 |
r_mcbond_it | 1.21 |
r_mcbond_other | 1.208 |
r_angle_other_deg | 1.061 |
r_chiral_restr | 0.115 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6540 |
Nucleic Acid Atoms | |
Solvent Atoms | 756 |
Heterogen Atoms | 105 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data collection |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
HKL-2000 | phasing |