6GIR
Arabidopsis thaliana cytosolic seryl-tRNA synthetase
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3QNE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 291 | Hanging drop vapor diffusion method; mixture of 4 uL 3.9 mg/mL protein solution, 2 uL of precipitating solution (0.2 M MgCl2, 0.1 M Tris pH 7, 30%(w/v) PEG 4000) and 1uL of additive solution (0.6 M MgCl2) at 291 K. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 46.55 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 92.127 | α = 90 |
b = 45.607 | β = 97.74 |
c = 103.548 | γ = 90 |
Symmetry | |
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Space Group | I 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 | PIXEL | DECTRIS PILATUS 2M | 2018-03-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ELETTRA BEAMLINE 5.2R | 1 | ELETTRA | 5.2R |
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 | 2.343 | 73.28 | 96.06 | 0.127 | 5.29 | 2.6 | 16605 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.343 | 2.44 |
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 | 3qne | 2.343 | 30.28 | 16605 | 891 | 96.06 | 0.21463 | 0.21126 | 0.27845 | RANDOM | 42.021 |
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] | |
5.15 | 2.43 | -3.14 | -2.58 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.003 |
r_dihedral_angle_3_deg | 16.165 |
r_dihedral_angle_4_deg | 13.852 |
r_dihedral_angle_1_deg | 8.472 |
r_long_range_B_refined | 6.705 |
r_long_range_B_other | 6.686 |
r_scangle_other | 4.309 |
r_mcangle_it | 4.233 |
r_mcangle_other | 4.232 |
r_mcbond_it | 2.607 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3177 |
Nucleic Acid Atoms | |
Solvent Atoms | 71 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CrysalisPro | data reduction |
SCALA | data scaling |
AMoRE | phasing |