2QBT
Structural Studies Reveal The Inactivation of E. coli L-aspartate aminotransferase by (S)-4,5-amino-dihydro-2-thiophenecarboxylic acid (SADTA) via Two Mechanisms (at pH 8.0)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1AMQ | pdb entry 1AMQ |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 8 | 298 | 25 mM potassium phosphate, 43% saturated ammonium sulfate, 20 mM SADTA, pH 8.0, EVAPORATION, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.95 | 58.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 154.149 | α = 90 |
b = 84.76 | β = 90 |
c = 78.951 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2005-02-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 14-BM-C | 0.9 | APS | 14-BM-C |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.75 | 24.8 | 98.2 | 0.065 | 12.5 | 4.7 | 48869 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.75 | 1.81 | 99.5 | 0.589 | 2.3 | 4.6 | 5143 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | 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 entry 1AMQ | 1.75 | 24.8 | 2.3 | 48869 | 2612 | 98.18 | 0.15093 | 0.14883 | 0.19031 | RANDOM | 24.359 |
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] | |
-1.04 | 1.07 | -0.03 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.679 |
r_dihedral_angle_4_deg | 18.663 |
r_dihedral_angle_3_deg | 14.028 |
r_dihedral_angle_1_deg | 6.514 |
r_scangle_it | 3.834 |
r_scbond_it | 2.623 |
r_mcangle_it | 1.639 |
r_angle_refined_deg | 1.486 |
r_mcbond_it | 1.052 |
r_nbtor_refined | 0.308 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3077 |
Nucleic Acid Atoms | |
Solvent Atoms | 410 |
Heterogen Atoms | 103 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
ADSC | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |