6N9A
Crystal Structure of Thermotoga maritima threonylcarbamoyladenosine biosynthesis complex TsaB2D2E2 bound to ATP and carboxy-AMP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 2 uL sample solution containing 3.1 mg/mL protein, 50 mM Tris (pH 7.5), 50 mM NaCl, 1 mM ATP and 0.1 mM MgCl2 with 2 uL reservoir solution containing 8% polyethylene glycol (PEG) 400, 100 mM KCl, 50 mM MES (pH 6.0) and 0.8 mM MgCl2 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.38 | 63.64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 124.053 | α = 90 |
b = 124.053 | β = 90 |
c = 119.035 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 | 80 | CCD | MARMOSAIC 325 mm CCD | 2016-12-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL14-1 | 1.19499 | SSRL | BL14-1 |
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) | 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 | 2.5 | 107.43 | 98.8 | 0.122 | 0.13 | 0.042 | 6.1 | 9 | 36821 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.5 | 2.54 | 84.2 | 1.886 | 2.297 | 1.281 | 0.182 | 2.6 |
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 | 2A6A | 2.5 | 42.94 | 31308 | 1787 | 89.12 | 0.12681 | 0.12185 | 0.21438 | RANDOM | 76.982 |
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] | |
-1.66 | -0.83 | -1.66 | 5.38 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 47.744 |
r_sphericity_bonded | 43.476 |
r_dihedral_angle_2_deg | 33.739 |
r_dihedral_angle_3_deg | 17.962 |
r_long_range_B_refined | 17.051 |
r_long_range_B_other | 17.047 |
r_dihedral_angle_4_deg | 16.691 |
r_scangle_other | 16.523 |
r_mcangle_it | 13.933 |
r_mcangle_other | 13.932 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5490 |
Nucleic Acid Atoms | |
Solvent Atoms | 161 |
Heterogen Atoms | 105 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data scaling |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
PHENIX | phasing |