8BCQ
N-terminal domain of Plasmodium berghei glutamyl-tRNA synthetase (native crystal structure)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 298 | Protein concentration: 6 to 9 mg/mL 0.1 M HEPS-NaOH pH 7.5, 1.4-1.5 M ammonium sulfate, 20% (v/v) glycerol and using microseeding. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.16 | 61.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 129.979 | α = 90 |
b = 88.683 | β = 106.13 |
c = 169.284 | 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 | PIXEL | DECTRIS EIGER X 16M | Kirkpatrick-Baez mirrors | 2020-06-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | 0.97857 | SOLEIL | PROXIMA 1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.7 | 47.16 | 99.69 | 0.07188 | 0.07767 | 0.02919 | 0.999 | 14.81 | 7 | 50722 | 82.29 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.703 | 2.799 | 97.73 | 1.181 | 1.277 | 0.4809 | 0.759 | 1.47 | 6.9 |
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 (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 8BHD | 2.7 | 47.16 | 1.35 | 50688 | 2535 | 99.71 | 0.201 | 0.1993 | 0.2336 | 121.4 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 11.726 |
f_angle_d | 0.3761 |
f_chiral_restr | 0.0389 |
f_plane_restr | 0.0023 |
f_bond_d | 0.0015 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8433 |
Nucleic Acid Atoms | |
Solvent Atoms | 16 |
Heterogen Atoms | 154 |
Software
Software | |
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Software Name | Purpose |
MxCuBE | data collection |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | phasing |
PHENIX | refinement |