6EQO
Tri-functional propionyl-CoA synthase of Erythrobacter sp. NAP1 with bound NADP+ and phosphomethylphosphonic acid adenylate ester
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.9 | 291 | 1 part protein solution (10 mg/mL protein in 20 mM Tris-HCl, pH 7.9, 150 mM sodium chloride, 2 mM CoA, 2 mM NADP+, 2 mM beta,gamma-methylene-ATP) + 1 part buffer (0.1 M BisTris, pH 6.5, 0.2 M sodium acetate, 25% w/v PEG3350, 3% w/v trimethylamine N-oxide dihydrate) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.63 | 53.16 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 383.414 | α = 90 |
b = 86.74 | β = 108.89 |
c = 133.958 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | 100 | PIXEL | DECTRIS PILATUS3 6M | 2016-07-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.97625 | ESRF | ID29 |
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 | 2.7 | 46.18 | 97.9 | 0.212 | 0.255 | 0.14 | 0.958 | 4.2 | 3.1 | 112000 | 46.49 |
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 | 2.7 | 2.75 | 94.2 | 0.886 | 1.092 | 0.626 | 0.189 | 2.7 |
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 | 2.7 | 46.179 | 1.34 | 111918 | 2007 | 97.59 | 0.1914 | 0.1907 | 0.2289 | 52.815 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 21.735 |
f_angle_d | 0.765 |
f_chiral_restr | 0.285 |
f_bond_d | 0.006 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 27636 |
Nucleic Acid Atoms | |
Solvent Atoms | 432 |
Heterogen Atoms | 150 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
MOSFLM | data collection |
Aimless | data scaling |
PHENIX | phasing |
PDB_EXTRACT | data extraction |
iMOSFLM | data reduction |