1V4P
Crystal structure of Alanyl-tRNA Synthetase from Pyrococcus horikoshii OT3
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 6.3 | 291 | PEG 4000, pH 6.3, Microbatch, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 40.73 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.802 | α = 90 |
b = 97.861 | β = 96.51 |
c = 60.872 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | IMAGE PLATE | RIGAKU RAXIS V | 2003-10-03 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | RIGAKU JUPITER 210 | 2003-10-31 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL26B1 | 1.0 | SPring-8 | BL26B1 |
2 | SYNCHROTRON | SPRING-8 BEAMLINE BL26B1 | 1.0, 0.9792, 0.9795 | SPring-8 | BL26B1 |
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 | ||||||||
1,2 | 1.45 | 50 | 99.9 | 0.051 | 3.7 | 88112 | 88112 | 17.7 |
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) | |||||||||||
1.45 | 1.5 | 99.5 | 0.453 | 2.3 | 3.6 | 8751 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | MAD | THROUGHOUT | 1.45 | 38.04 | 87972 | 87972 | 4409 | 99.9 | 0.207 | 0.207 | 0.206 | 0.227 | random | 18.8 |
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] | |
1.81 | -0.47 | -1.33 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_angle_deg | 1.297 |
c_bond_d | 0.0045 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3724 |
Nucleic Acid Atoms | |
Solvent Atoms | 599 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
SCALEPACK | data scaling |
SOLVE | phasing |
CNS | refinement |
HKL-2000 | data reduction |