8A8G
ATP sulfurylase from Methanothermococcus thermolithotrophicus - orthorhombic form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1V47 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 291 | Purified ATPS sulfurylase from Methanothermococcus thermolithotrophicus was concentrated to 14 mg.ml-1 in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol, 2 mM dithiothreitol, and 150 mM NaCl. Crystals were obtained by mixing 0.7 ul of the sample with 0.7 ul of 35 % w/v Pentaerythritol ethoxylate (15/4 EO/OH), and 100 mM 2-(N-morpholino)ethanesulfonic acid (MES) pH 6.5 in a 96-Well MRC 2-drop crystallization plates in polystyrene (SWISSCI) containing 90 ul of crystallization solution in the reservoir. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.8 | 67.61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 55.705 | α = 90 |
b = 154.457 | β = 90 |
c = 157.575 | γ = 90 |
Symmetry | |
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Space Group | I 2 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 EIGER X 16M | 2019-02-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | 1.00000 | 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 | 1.97 | 78.79 | 93.2 | 0.151 | 0.157 | 0.042 | 0.998 | 12.7 | 13.7 | 28197 | 37.7 |
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 | 1.97 | 2.22 | 62.3 | 1.74 | 1.806 | 0.483 | 0.641 | 1.6 | 13.9 |
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 | THROUGHOUT | 1V47 | 1.97 | 49.73 | 1.34 | 28185 | 1425 | 58.17 | 0.19 | 0.1885 | 0.2179 | 42.81 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3136 |
Nucleic Acid Atoms | |
Solvent Atoms | 208 |
Heterogen Atoms | 49 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
autoPROC | data reduction |
autoPROC | data scaling |
PHENIX | phasing |