3G98
Crystal Structure of the C-Ala domain from Aquifex aeolicus alanyl-tRNA synthetase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 295 | 30% PEG6000, 100 mM MES, 1 M LiCl, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.88 | 34.69 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.74 | α = 90 |
b = 54.506 | β = 90 |
c = 66.256 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | MARMOSAIC 325 mm CCD | Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) | 2007-05-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.98 | SSRL | BL11-1 |
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 | 1.85 | 50 | 98.6 | 0.053 | 0.053 | 46.8 | 11.4 | 16315 | 16087 | 1 | 1 | 26.8 |
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) | ||||||||||
1.85 | 1.92 | 86 | 0.405 | 0.405 | 3.3 | 6.1 | 1375 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.85 | 40.28 | 2 | 16315 | 15234 | 808 | 99.22 | 0.216 | 0.18598 | 0.18423 | 0.21871 | RANDOM | 29.535 |
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] | |
1.01 | -0.7 | -0.31 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.152 |
r_dihedral_angle_4_deg | 17.427 |
r_dihedral_angle_3_deg | 11.777 |
r_scangle_it | 10.131 |
r_scbond_it | 7.357 |
r_mcangle_it | 6.246 |
r_mcbond_it | 5.474 |
r_dihedral_angle_1_deg | 4.474 |
r_angle_refined_deg | 0.984 |
r_nbtor_refined | 0.321 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1718 |
Nucleic Acid Atoms | |
Solvent Atoms | 139 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
SOLVE | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |