6XZ0
Crystal structure of spectinomycin adenyltransferase AAD(9) from Enterococcus faecialis with spectinomycin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6SXJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 281 | 10% w/v PEG 4000, 20% v/v glycerol, 0.02 M of each alcohol (0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol), 0.1 M bicine/Trizma base pH 8.5) were soaked with 10 mM ATP, 10 mM magnesium and spectinomycin powder for 30 seconds |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.46 | 60 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 99.561 | α = 90 |
b = 99.561 | β = 90 |
c = 61.327 | γ = 90 |
Symmetry | |
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Space Group | I 4 |
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 16M | 2019-04-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.97950 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 2.8 | 49.8 | 99.6 | 0.1 | 0.1 | 0.9 | 19.8 | 22.9 | 7509 | 69.18 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.8 | 2.9 | 99.5 | 1.5 | 0.9 |
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 | 6SXJ | 2.8 | 49.78 | 1.35 | 7480 | 385 | 99.57 | 0.2486 | 0.245 | 0.3026 | 75.88 |
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 | 2.903 |
f_angle_d | 0.6341 |
f_chiral_restr | 0.0474 |
f_plane_restr | 0.0042 |
f_bond_d | 0.0029 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2047 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 23 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
Coot | model building |
PHENIX | refinement |