3DYD
Human Tyrosine Aminotransferase
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1BW0 | PDB ENTRY 1BW0 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 293 | 30% MPD, 0.1M Na-Acetate pH 4.6, 3mM PLP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.69 | 54.24 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 154.42 | α = 90 |
b = 91.59 | β = 106.18 |
c = 75.57 | 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 QUANTUM 4 | 2008-06-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | 0.93300 | ESRF | ID14-2 |
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 | 2.3 | 40 | 99.5 | 0.115 | 0.157 | 10.7 | 3.8 | 44821 | 44821 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.3 | 2.4 | 99.3 | 0.492 | 0.55 | 3.3 | 3.6 | 5284 |
Refinement
Statistics | |||||||||||||||||||
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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 1BW0 | 2.3 | 36.91 | 2 | 42574 | 42574 | 2241 | 100 | 0.22158 | 0.21949 | 0.26088 | RANDOM | 11.102 |
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] | |
-0.1 | 0.14 | -0.61 | 0.79 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.602 |
r_dihedral_angle_4_deg | 18.147 |
r_dihedral_angle_3_deg | 14.77 |
r_dihedral_angle_1_deg | 7.28 |
r_scangle_it | 1.581 |
r_angle_refined_deg | 1.155 |
r_scbond_it | 0.975 |
r_angle_other_deg | 0.85 |
r_mcangle_it | 0.605 |
r_mcbond_it | 0.311 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6043 |
Nucleic Acid Atoms | |
Solvent Atoms | 206 |
Heterogen Atoms | 30 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MxCuBE | data collection |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |