3PA9
Mechanism of inactivation of E. coli aspartate aminotransferase by (S)-4-amino-4,5-dihydro-2-furancarboxylic acid (S-ADFA) pH 7.5
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 | VAPOR DIFFUSION | 7.5 | 297 | Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, temperature 297K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.99 | 58.85 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 154.135 | α = 90 |
b = 85.532 | β = 90 |
c = 79.033 | γ = 90 |
Symmetry | |
---|---|
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 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 14-BM-C | 0.97 | APS | 14-BM-C |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.7 | 77.2 | 97.7 | 67102 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1AMQ | 1.7 | 77.15 | 2 | 67102 | 53395 | 2851 | 97.83 | 0.15012 | 0.14827 | 0.18519 | RANDOM | 23.043 |
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] | |
-0.59 | 0.55 | 0.04 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.14 |
r_dihedral_angle_4_deg | 16.314 |
r_dihedral_angle_3_deg | 13.484 |
r_dihedral_angle_1_deg | 5.6 |
r_scangle_it | 3.552 |
r_scbond_it | 2.445 |
r_mcangle_it | 1.543 |
r_angle_refined_deg | 1.269 |
r_mcbond_it | 0.974 |
r_nbtor_refined | 0.307 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3069 |
Nucleic Acid Atoms | |
Solvent Atoms | 420 |
Heterogen Atoms | 110 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
CNS | refinement |
HKL-2000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CNS | phasing |