8FO0
The structure of a crystallizable variant of E. coli pyruvate formate-lyase activating enzyme bound to a partially cleaved SAM molecule
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3C8F |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 300 | 4 uL of protein (10 mg/mL PFL-AE-CCR8 in 25 mM Tris, 500 200 mM KCl, with 3.5 mM SAM, 5.0 mM 7-mer RVSAYAV peptide, 0.13% glycerol, and 2.5 mM DTT) added to 1 uL of crystallization reservoir solution (30% PEG 3350, 100 mM Tris, pH 8.5) in hanging drop format over a reservoir containing of 50 uL of crystallization reservoir solution. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.04 | 39.79 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.58 | α = 90 |
b = 58.551 | β = 90 |
c = 84.484 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2016-12-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.542 |
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 | 1.69 | 34.26 | 99.66 | 0.06465 | 0.06748 | 0.01912 | 0.999 | 23.76 | 11.7 | 26396 | 26.46 |
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 | 1.69 | 1.753 | 97.15 | 0.683 | 0.721 | 0.2236 | 0.898 | 1.8 | 8.5 |
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 | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.69 | 34.26 | 1.34 | 26383 | 1294 | 99.68 | 0.1653 | 0.1642 | 0.188 | Random selection within each resolution shell | 36.31 |
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 | 16.8313 |
f_angle_d | 0.8613 |
f_chiral_restr | 0.2923 |
f_bond_d | 0.0326 |
f_plane_restr | 0.0045 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1972 |
Nucleic Acid Atoms | |
Solvent Atoms | 137 |
Heterogen Atoms | 36 |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |
Coot | model building |