4AOK
Conformational dynamics of aspartate alpha-decarboxylase active site revealed by protein-ligand complexes: 1-methyl-L-aspartate complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1AW8 | PDB ENTRY 1AW8 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 4.2 | 5 MG/ML ASPARTATE-ALPHA-DECARBOXYLASE IN 1.5 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE, PH 3.8 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51.27 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 71.3 | α = 90 |
b = 71.3 | β = 90 |
c = 215.9 | γ = 120 |
Symmetry | |
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Space Group | P 61 2 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 | PIXEL | DECTRIS PILATUS 6M | 2011-02-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | Diamond | I24 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.5 | 53.98 | 99.2 | 0.09 | 15.4 | 9.5 | 52548 | 19.05 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.5 | 1.58 | 99.1 | 1.48 | 1.7 | 9.1 |
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 | PDB ENTRY 1AW8 | 1.5 | 61.72 | 49762 | 2665 | 98.92 | 0.14619 | 0.14438 | 0.1796 | RANDOM | 18.296 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.41 | 0.21 | 0.41 | -0.62 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 34.69 |
r_dihedral_angle_2_deg | 29.718 |
r_dihedral_angle_4_deg | 16.024 |
r_sphericity_bonded | 12.855 |
r_dihedral_angle_3_deg | 12.481 |
r_rigid_bond_restr | 7.408 |
r_dihedral_angle_1_deg | 6.744 |
r_angle_refined_deg | 2.143 |
r_angle_other_deg | 1.159 |
r_chiral_restr | 0.152 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1874 |
Nucleic Acid Atoms | |
Solvent Atoms | 178 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |