8SLH
Crystal Structure of Glycine tRNA ligase from Mycobacterium thermoresistibile (AMP bound, hexagonal form)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 8SLD |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 291 | JCSG+ H8: 25% (w/v) PEG 3350, 0.2M NaCl, 0.1M Bis-Tris pH 5.5, MythA.19107.a.A1.PW39162 at 17 mg/mL. Plate: Clover 1/12/2023 AMP, H10. Puck: PSL-1508, Cryo: 15% PEG200 + 85% crystallant. 2mM AMP added prior to crystallization. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.67 | 53.95 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 126.254 | α = 90 |
b = 126.254 | β = 90 |
c = 127.896 | γ = 120 |
Symmetry | |
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Space Group | P 61 2 2 |
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 EIGER2 XE 9M | 2022-02-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 19-ID | 0.9795 | NSLS-II | 19-ID |
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 | 3.05 | 44.92 | 99.9 | 0.121 | 0.124 | 0.028 | 0.999 | 20.5 | 19.6 | 12003 |
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 | 3.05 | 3.26 | 100 | 1.789 | 1.833 | 0.399 | 0.883 | 20.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 3.05 | 41.55 | 1.15 | 11941 | 592 | 99.74 | 0.2329 | 0.23 | 0.2879 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 11.412 |
f_angle_d | 0.525 |
f_chiral_restr | 0.041 |
f_plane_restr | 0.005 |
f_bond_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2933 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 24 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
Aimless | data scaling |
XDS | data reduction |
PHASER | phasing |