6PT8
Crystal Structure of CobT from Methanocaldococcus jannaschii in complex with Adenine Alpha-Ribotide and Nicotinic Acid
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 298 | Crystals formed by mixing 1:1 ratio of 13.3 mg/mL protein solution with well solution containing 100 mM 4-(2-Hydroxyethyl)-1-piperazinepropanesulfonic acid (HEPPS) pH 8.5 and 22% (w/v) PEG 8K. 1 mM adenine and 50 mM Sodium/Potassium Phosphate pH 7.0 were added to protein prior to mixing with well solution. Substrates were captured in lattice prior to freezing by soaking crystals in 20% (w/v) ethylene glycol, 100 mM HEPPS pH 8.5, 22% (w/v) PEG 8K, 25 mM sodium/potassium phosophate pH 7.0, 1 mM nicotinic acid mononucleotide, and 1 mM adenine for 30 minutes. Crystals were then soaked in the same solution, but with 30% PEG 8K instead of 20% ethylene glycol and 20% PEG 8K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.06 | 40.37 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.39 | α = 90 |
b = 138.64 | β = 108.32 |
c = 51.15 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 PILATUS3 X 6M | 2018-08-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97934 | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.4 | 41.973 | 98.95 | 0.09626 | 12.18 | 6.8 | 118689 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.4 | 1.45 | 98.98 | 0.6674 | 2.92 | 6.8 |
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 | 3L0Z | 1.4 | 41.973 | 1.36 | 118680 | 5933 | 98.85 | 0.1542 | 0.1531 | 0.1748 | 18.8823 |
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 | 5307 |
Nucleic Acid Atoms | |
Solvent Atoms | 460 |
Heterogen Atoms | 106 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |